GENE
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int64 699
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TYMS | 7 | LKB1 KO, NF1 KO, NF2 KO, PBRM1 KO, PTEN KO, TP53 KO, TP53BP1 KO | 7,298 | TYMS | thymidylate synthetase | Homo sapiens (human) | Thymidylate synthase catalyzes the methylation of deoxyuridylate to deoxythymidylate using, 10-methylenetetrahydrofolate (methylene-THF) as a cofactor. This function maintains the dTMP (thymidine-5-prime monophosphate) pool critical for DNA replication and repair. The enzyme has been of interest as a target for cancer chemotherapeutic agents. It is considered to be the primary site of action for 5-fluorouracil, 5-fluoro-2-prime-deoxyuridine, and some folate analogs. Expression of this gene and that of a naturally occurring antisense transcript, mitochondrial enolase superfamily member 1 (GeneID:55556), vary inversely when cell-growth progresses from late-log to plateau phase. Polymorphisms in this gene may be associated with etiology of neoplasia, including breast cancer, and response to chemotherapy. [provided by RefSeq, Aug 2017] | DKCD, HST422, TMS, TS, thymidylate synthase, TSase |
UBE2T | 6 | CDH1 KO, LKB1 KO, NF1 KO, NF2 KO, PBRM1 KO, TP53BP1 KO | 29,089 | UBE2T | ubiquitin conjugating enzyme E2 T | Homo sapiens (human) | The protein encoded by this gene catalyzes the covalent attachment of ubiquitin to protein substrates. Defects in this gene have been associated with Fanconi anemia of complementation group T. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015] | FANCT, HSPC150, PIG50, ubiquitin-conjugating enzyme E2 T, E2 ubiquitin-conjugating enzyme T, HSPC150 protein similar to ubiquitin-conjugating enzyme, cell proliferation-inducing gene 50 protein, ubiquitin carrier protein T, ubiquitin conjugating enzyme E2T, ubiquitin-conjugating enzyme E2T (putative), ubiquitin-protein ligase T |
BRIP1 | 5 | LKB1 KO, NF1 KO, NF2 KO, PBRM1 KO, VHL KO | 83,990 | BRIP1 | BRCA1 interacting DNA helicase 1 | Homo sapiens (human) | The protein encoded by this gene is a member of the RecQ DEAH helicase family and interacts with the BRCT repeats of breast cancer, type 1 (BRCA1). The bound complex is important in the normal double-strand break repair function of breast cancer, type 1 (BRCA1). This gene may be a target of germline cancer-inducing mutations. [provided by RefSeq, Jul 2008] | BACH1, FANCJ, OF, Fanconi anemia group J protein, ATP-dependent RNA helicase BRIP1, BRCA1 interacting helicase 1, BRCA1 interacting protein C-terminal helicase 1, BRCA1-associated C-terminal helicase 1, BRCA1-binding helicase-like protein BACH1, BRCA1/BRCA2-associated helicase 1, DNA 5'-3' helicase FANCJ, FANCJ helicase |
DDX19A | 5 | ARID1A KD, CDH1 KO, NF2 KO, PBRM1 KO, RB1 KO | 55,308 | DDX19A | DEAD-box helicase 19A | Homo sapiens (human) | null | DDX19-DDX19L, DDX19L, ATP-dependent RNA helicase DDX19A, DDX19-like protein, DEAD (Asp-Glu-Ala-As) box polypeptide 19A, DEAD (Asp-Glu-Ala-Asp) box polypeptide 19A, DEAD box protein 19A, RNA helicase |
PPP2R3C | 5 | CDH1 KO, LKB1 KO, NF2 KO, RB1 KO, VHL KO | 55,012 | PPP2R3C | protein phosphatase 2 regulatory subunit B''gamma | Homo sapiens (human) | This gene encodes a regulatory subunit of the serine/threonine phosphatase, protein phosphatase 2. This protein is localized to both nuclear and cytoplasmic regions depending on cell cycle phase. Homozygous conditional knockout mice for this gene exhibit reduced numbers and impaired proliferation of immune system B cells. This protein may regulate the expression of the P-glycoprotein ATP-binding cassette transporter through its phosphatase activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015] | C14orf10, G4-1, G5pr, GDRM, MEGD, SPGF36, serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma, protein phosphatase 2 (formerly 2A), regulatory subunit B'', protein phosphatase 2, regulatory subunit B'', gamma, protein phosphatase subunit G5PR, rhabdomyosarcoma antigen MU-RMS-40.6A, rhabdomyosarcoma antigen Mu-RMS-40.6C |
RPRD1B | 5 | LKB1 KO, NF1 KO, PTEN KO, TP53 KO, VHL KO | 58,490 | RPRD1B | regulation of nuclear pre-mRNA domain containing 1B | Homo sapiens (human) | null | C20orf77, CREPT, K-H, Kub5-Hera, NET60, dJ1057B20.2, regulation of nuclear pre-mRNA domain-containing protein 1B, Ku70-binding protein 5-Hera, cell-cycle related and expression-elevated protein in tumor |
BPTF | 4 | ARID1A KD, KEAP1 KO, PBRM1 KO, TP53 KO | 2,186 | BPTF | bromodomain PHD finger transcription factor | Homo sapiens (human) | This gene was identified by the reactivity of its encoded protein to a monoclonal antibody prepared against brain homogenates from patients with Alzheimer's disease. Analysis of the original protein (fetal Alz-50 reactive clone 1, or FAC1), identified as an 810 aa protein containing a DNA-binding domain and a zinc finger motif, suggested it might play a role in the regulation of transcription. High levels of FAC1 were detected in fetal brain and in patients with neurodegenerative diseases. The protein encoded by this gene is actually much larger than originally thought, and it also contains a C-terminal bromodomain characteristic of proteins that regulate transcription during proliferation. The encoded protein is highly similar to the largest subunit of the Drosophila NURF (nucleosome remodeling factor) complex. In Drosophila, the NURF complex, which catalyzes nucleosome sliding on DNA and interacts with sequence-specific transcription factors, is necessary for the chromatin remodeling required for transcription. Two alternative transcripts encoding different isoforms have been described completely. [provided by RefSeq, Jul 2008] | FAC1, FALZ, NEDDFL, NURF301, nucleosome-remodeling factor subunit BPTF, bromodomain and PHD domain transcription factor, bromodomain and PHD finger-containing transcription factor, fetal Alz-50 clone 1 protein, fetal Alz-50 reactive clone 1, fetal Alzheimer antigen, nucleosome remodeling factor, large subunit |
FANCA | 4 | LKB1 KO, NF2 KO, PBRM1 KO, VHL KO | 2,175 | FANCA | FA complementation group A | Homo sapiens (human) | The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group A. Alternative splicing results in multiple transcript variants encoding different isoforms. Mutations in this gene are the most common cause of Fanconi anemia. [provided by RefSeq, Jul 2008] | FA, FA-H, FA1, FAA, FACA, FAH, FANCH, Fanconi anemia group A protein, Fanconi anemia complementation group A, Fanconi anemia, complementation group H, Fanconi anemia, type 1 |
FANCD2 | 4 | CDH1 KO, NF2 KO, PBRM1 KO, TP53BP1 KO | 2,177 | FANCD2 | FA complementation group D2 | Homo sapiens (human) | The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group D2. This protein is monoubiquinated in response to DNA damage, resulting in its localization to nuclear foci with other proteins (BRCA1 AND BRCA2) involved in homology-directed DNA repair. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016] | FA-D2, FA4, FACD, FAD, FAD2, FANCD, Fanconi anemia group D2 protein, Fanconi anemia complementation group D2 |
FANCF | 4 | CDH1 KO, LKB1 KO, NF2 KO, PBRM1 KO | 2,188 | FANCF | FA complementation group F | Homo sapiens (human) | The Fanconi anemia complementation group (FANC) currently includes FANCA, FANCB, FANCC, FANCD1 (also called BRCA2), FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ (also called BRIP1), FANCL, FANCM and FANCN (also called PALB2). The previously defined group FANCH is the same as FANCA. Fanconi anemia is a genetically heterogeneous recessive disorder characterized by cytogenetic instability, hypersensitivity to DNA crosslinking agents, increased chromosomal breakage, and defective DNA repair. The members of the Fanconi anemia complementation group do not share sequence similarity; they are related by their assembly into a common nuclear protein complex. This gene encodes the protein for complementation group F. [provided by RefSeq, Jul 2008] | FAF, Fanconi anemia group F protein, Fanconi anemia complementation group F |
MCM9 | 4 | LKB1 KO, NF2 KO, VHL KO, TP53BP1 KO | 254,394 | MCM9 | minichromosome maintenance 9 homologous recombination repair factor | Homo sapiens (human) | The protein encoded by this gene is a member of the mini-chromosome maintenance (MCM) protein family that are essential for the initiation of eukaryotic genome replication. Binding of this protein to chromatin has been shown to be a pre-requisite for recruiting the MCM2-7 helicase to DNA replication origins. This protein also binds, and is a positive regulator of, the chromatin licensing and DNA replication factor 1, CDT1. [provided by RefSeq, Nov 2010] | C6orf61, MCMDC1, ODG4, dJ329L24.1, dJ329L24.3, DNA helicase MCM9, DNA replication licensing factor MCM9, mini-chromosome maintenance deficient domain-containing protein 1, minichromosome maintenance complex component 9 |
SDHB | 4 | BAP1 KO, LKB1 KO, PBRM1 KO, VHL KO | 6,390 | SDHB | succinate dehydrogenase complex iron sulfur subunit B | Homo sapiens (human) | Complex II of the respiratory chain, which is specifically involved in the oxidation of succinate, carries electrons from FADH to CoQ. The complex is composed of four nuclear-encoded subunits and is localized in the mitochondrial inner membrane. The iron-sulfur subunit is highly conserved and contains three cysteine-rich clusters which may comprise the iron-sulfur centers of the enzyme. Sporadic and familial mutations in this gene result in paragangliomas and pheochromocytoma, and support a link between mitochondrial dysfunction and tumorigenesis. [provided by RefSeq, Jul 2008] | CWS2, IP, MC2DN4, PGL4, PPGL4, SDH, SDH1, SDH2, SDHIP, succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial, iron-sulfur subunit of complex II, malate dehydrogenase [quinone] iron-sulfur subunit, succinate dehydrogenase complex, subunit B, iron sulfur (Ip) |
USPL1 | 4 | BAP1 KO, NF2 KO, PTEN KO, TP53BP1 KO | 10,208 | USPL1 | ubiquitin specific peptidase like 1 | Homo sapiens (human) | null | C13orf22, D13S106E, bA121O19.1, SUMO-specific isopeptidase USPL1, USP-like 1, highly charged protein, ubiquitin-specific peptidase-like protein 1 |
ATG9A | 3 | LKB1 KO, NF1 KO, VHL KO | 79,065 | ATG9A | autophagy related 9A | Homo sapiens (human) | null | APG9L1, MGD3208, mATG9, autophagy-related protein 9A, APG9 autophagy 9-like 1, APG9-like 1, ATG9 autophagy related 9 homolog A, autophagy 9-like 1 protein |
C16orf72 | 3 | ARID1A KD, BAP1 KO, NF1 KO | 29,035 | HAPSTR1 | HUWE1 associated protein modifying stress responses | Homo sapiens (human) | null | C16orf72, PRO0149, TAPR1, HUWE1-associated protein modifying stress responses 1, Telomere Attrition and p53 Response 1, UPF0472 protein C16orf72, telomere attrition and p53 response 1 protein |
COQ2 | 3 | BAP1 KO, KEAP1 KO, RB1 KO | 27,235 | COQ2 | coenzyme Q2, polyprenyltransferase | Homo sapiens (human) | This gene encodes an enzyme that functions in the final steps in the biosynthesis of CoQ (ubiquinone), a redox carrier in the mitochondrial respiratory chain and a lipid-soluble antioxidant. This enzyme, which is part of the coenzyme Q10 pathway, catalyzes the prenylation of parahydroxybenzoate with an all-trans polyprenyl group. Mutations in this gene cause coenzyme Q10 deficiency, a mitochondrial encephalomyopathy, and also COQ2 nephropathy, an inherited form of mitochondriopathy with primary renal involvement. [provided by RefSeq, Oct 2009] | CL640, COQ10D1, MSA1, PHB:PPT, 4-hydroxybenzoate polyprenyltransferase, mitochondrial, 4-HB polyprenyltransferase, 4-hydroxybenzoate decaprenyltransferase, PHB:polyprenyltransferase, coenzyme Q2 4-hydroxybenzoate polyprenyltransferase, coenzyme Q2 homolog, prenyltransferase, para-hydroxybenzoate-polyprenyltransferase, mitochondrial |
FAM106A | 3 | LKB1 KO, NF1 KO, PTEN KO | 80,039 | FAM106A | family with sequence similarity 106 member A | Homo sapiens (human) | null | protein FAM106A |
FBXW11 | 3 | LKB1 KO, NF1 KO, VHL KO | 23,291 | FBXW11 | F-box and WD repeat domain containing 11 | Homo sapiens (human) | This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbws class and, in addition to an F-box, contains multiple WD40 repeats. This gene contains at least 14 exons, and its alternative splicing generates 3 transcript variants diverging at the presence/absence of two alternate exons. [provided by RefSeq, Jul 2008] | BTRC2, BTRCP2, FBW1B, FBXW1B, Fbw11, Hos, NEDJED, F-box/WD repeat-containing protein 11, F-box and WD repeats protein beta-TrCP2, F-box and WD-40 domain protein 11, F-box and WD-40 domain protein 1B, F-box protein Fbw1b, F-box/WD repeat-containing protein 1B, beta-transducin repeat-containing protein 2, homologous to Slimb protein |
NDUFC1 | 3 | NF1 KO, PBRM1 KO, PTEN KO | 4,717 | NDUFC1 | NADH:ubiquinone oxidoreductase subunit C1 | Homo sapiens (human) | The encoded protein is a subunit of the NADH:ubiquinone oxidoreductase (complex I), the first enzyme complex in the electron transport chain located in the inner mitochondrial membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010] | KFYI, NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial, CI-KFYI, NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 1, 6kDa, NADH-ubiquinone oxidoreductase KFYI subunit, complex I KFYI subunit, complex I-KFYI |
PMVK | 3 | BAP1 KO, NF1 KO, NF2 KO | 10,654 | PMVK | phosphomevalonate kinase | Homo sapiens (human) | This gene encodes a peroxisomal enzyme that is a member of the galactokinase, homoserine kinase, mevalonate kinase, and phosphomevalonate kinase (GHMP) family of ATP-dependent enzymes. The encoded protein catalyzes the conversion of mevalonate 5-phosphate to mevalonate 5-diphosphate, which is the fifth step in the mevalonate pathway of isoprenoid biosynthesis. Mutations in this gene are linked to certain types of porokeratosis including disseminated superficial porokeratosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017] | HUMPMKI, PMK, PMKA, PMKASE, POROK1, testis tissue sperm-binding protein Li 95mP |
PRDX1 | 3 | NF1 KO, NF2 KO, PBRM1 KO | 5,052 | PRDX1 | peroxiredoxin 1 | Homo sapiens (human) | This gene encodes a member of the peroxiredoxin family of antioxidant enzymes, which reduce hydrogen peroxide and alkyl hydroperoxides. The encoded protein may play an antioxidant protective role in cells, and may contribute to the antiviral activity of CD8(+) T-cells. This protein may have a proliferative effect and play a role in cancer development or progression. Four transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jan 2011] | MSP23, NKEF-A, NKEFA, PAG, PAGA, PAGB, PRX1, PRXI, TDPX2, peroxiredoxin-1, epididymis secretory sperm binding protein, natural killer cell-enhancing factor A, natural killer-enhancing factor A, proliferation-associated gene A, proliferation-associated gene protein, thioredoxin peroxidase 2, thioredoxin-dependent peroxide reductase 2, thioredoxin-dependent peroxiredoxin 1 |
PRKRA | 3 | LKB1 KO, NF1 KO, VHL KO | 8,575 | PRKRA | protein activator of interferon induced protein kinase EIF2AK2 | Homo sapiens (human) | This gene encodes a protein kinase activated by double-stranded RNA which mediates the effects of interferon in response to viral infection. Mutations in this gene have been associated with dystonia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2008] | DYT16, HSD14, PACT, RAX, interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X, PKR-associating protein X, protein activator of the interferon-induced protein kinase, protein kinase, interferon-inducible double-stranded RNA-dependent activator |
SLC25A33 | 3 | LKB1 KO, VHL KO, TP53BP1 KO | 84,275 | SLC25A33 | solute carrier family 25 member 33 | Homo sapiens (human) | SLC25A33 belongs to the SLC25 family of mitochondrial carrier proteins (Haitina et al., 2006 [PubMed 16949250]).[supplied by OMIM, Mar 2008] | BMSC-MCP, PNC1, bone marrow stromal cell mitochondrial carrier protein, huBMSC-MCP, mitochondrial carrier protein, novel mitochondrial carrier protein, solute carrier family 25 (pyrimidine nucleotide carrier), member 33 |
UIMC1 | 3 | CDH1 KO, KEAP1 KO, NF1 KO | 51,720 | UIMC1 | ubiquitin interaction motif containing 1 | Homo sapiens (human) | This gene encodes a nuclear protein that interacts with Brca1 (breast cancer 1) in a complex to recognize and repair DNA lesions. This protein binds ubiquitinated lysine 63 of histone H2A and H2AX. This protein may also function as a repressor of transcription. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015] | RAP80, X2HRIP110, BRCA1-A complex subunit RAP80, receptor-associated protein 80, retinoid X receptor-interacting protein 110 |
UMPS | 3 | PBRM1 KO, RB1 KO, VHL KO | 7,372 | UMPS | uridine monophosphate synthetase | Homo sapiens (human) | This gene encodes a uridine 5'-monophosphate synthase. The encoded protein is a bifunctional enzyme that catalyzes the final two steps of the de novo pyrimidine biosynthetic pathway. The first reaction is carried out by the N-terminal enzyme orotate phosphoribosyltransferase which converts orotic acid to orotidine-5'-monophosphate. The terminal reaction is carried out by the C-terminal enzyme OMP decarboxylase which converts orotidine-5'-monophosphate to uridine monophosphate. Defects in this gene are the cause of hereditary orotic aciduria. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010] | OPRT, uridine 5'-monophosphate synthase, OMPdecase, OPRTase, UMP synthase, orotate phosphoribosyltransferase, orotidine 5'-phosphate decarboxylase |
ARID2 | 2 | LKB1 KO, NF2 KO | 196,528 | ARID2 | AT-rich interaction domain 2 | Homo sapiens (human) | This gene encodes a member of the AT-rich interactive domain (ARID)-containing family of DNA-binding proteins. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and chromatin structure modification. This protein functions as a subunit of the polybromo- and BRG1-associated factor or PBAF (SWI/SNF-B) chromatin remodeling complex which facilitates ligand-dependent transcriptional activation by nuclear receptors. Mutations in this gene are associated with hepatocellular carcinomas. A pseudogene of this gene is found on chromosome1. [provided by RefSeq, Dec 2016] | BAF200, CSS6, SMARCF3, ZIPZAP, p200, AT-rich interactive domain-containing protein 2, ARID domain-containing protein 2, AT rich interactive domain 2 (ARID, RFX-like), BRG1-associated factor 200, zinc finger protein with activation potential, zipzap/p200 |
BIRC6 | 2 | LKB1 KO, VHL KO | 57,448 | BIRC6 | baculoviral IAP repeat containing 6 | Homo sapiens (human) | This gene encodes a protein with a BIR (baculoviral inhibition of apoptosis protein repeat) domain and a UBCc (ubiquitin-conjugating enzyme E2, catalytic) domain. This protein inhibits apoptosis by facilitating the degradation of apoptotic proteins by ubiquitination. [provided by RefSeq, Jul 2008] | APOLLON, BRUCE, baculoviral IAP repeat-containing protein 6, BIR repeat-containing ubiquitin-conjugating enzyme, RING-type E3 ubiquitin transferase BIRC6, ubiquitin-conjugating BIR-domain enzyme apollon |
BUB1 | 2 | ARID1A KD, CDH1 KO | 699 | BUB1 | BUB1 mitotic checkpoint serine/threonine kinase | Homo sapiens (human) | This gene encodes a serine/threonine-protein kinase that play a central role in mitosis. The encoded protein functions in part by phosphorylating members of the mitotic checkpoint complex and activating the spindle checkpoint. This protein also plays a role in inhibiting the activation of the anaphase promoting complex/cyclosome. This protein may also function in the DNA damage response. Mutations in this gene have been associated with aneuploidy and several forms of cancer. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013] | BUB1A, BUB1L, MCPH30, hBUB1, mitotic checkpoint serine/threonine-protein kinase BUB1, BUB1 budding uninhibited by benzimidazoles 1 homolog, budding uninhibited by benzimidazoles 1 homolog, mitotic spindle checkpoint kinase, putative serine/threonine-protein kinase |
BZW1 | 2 | BAP1 KO, NF2 KO | 9,689 | BZW1 | basic leucine zipper and W2 domains 1 | Homo sapiens (human) | null | 5MP2, BZAP45, Nbla10236, eIF5-mimic protein 2, basic leucine zipper and W2 domain-containing protein 1, basic leucine-zipper protein BZAP45, putative protein product of Nbla10236 |
C12orf44 | 2 | LKB1 KO, VHL KO | 60,673 | ATG101 | autophagy related 101 | Homo sapiens (human) | null | C12orf44, autophagy-related protein 101, Atg13-interacting protein |
C1orf228 | 2 | CDH1 KO, VHL KO | 339,541 | ARMH1 | armadillo like helical domain containing 1 | Homo sapiens (human) | null | C1orf228, NCRNA00082, p40, armadillo-like helical domain containing protein 1, uncharacterized protein C1orf228 |
CAB39 | 2 | TP53 KO, VHL KO | 51,719 | CAB39 | calcium binding protein 39 | Homo sapiens (human) | null | CGI-66, MO25, calcium-binding protein 39, MO25alpha |
CAPRIN1 | 2 | CDH1 KO, VHL KO | 4,076 | CAPRIN1 | cell cycle associated protein 1 | Homo sapiens (human) | null | CONDCAC, GPIAP1, GPIP137, GRIP137, M11S1, NEDLAAD, RNG105, p137GPI, caprin-1, GPI-anchored membrane protein 1, GPI-anchored protein p137, GPI-p137, RNA granule protein 105, activation/proliferation-associated protein 1, caprin 1, cytoplasmic activation- and proliferation-associated protein 1, cytoplasmic activation/proliferation-associated protein-1, membrane component chromosome 11 surface marker 1 |
CHMP6 | 2 | ARID1A KD, TP53BP1 KO | 79,643 | CHMP6 | charged multivesicular body protein 6 | Homo sapiens (human) | This gene encodes a member of the chromatin-modifying protein/charged multivesicular body protein family. Proteins in this family are part of the ESCRT-III (endosomal sorting complex required for transport III) which degrades surface receptors, and in biosynthesis of endosomes. [provided by RefSeq, Mar 2012] | VPS20, chromatin-modifying protein 6, hVps20, vacuolar protein sorting-associated protein 20 |
CNKSR2 | 2 | NF1 KO, TP53 KO | 22,866 | CNKSR2 | connector enhancer of kinase suppressor of Ras 2 | Homo sapiens (human) | This gene encodes a multidomain protein that functions as a scaffold protein to mediate the mitogen-activated protein kinase pathways downstream from Ras. This gene product is induced by vitamin D and inhibits apoptosis in certain cancer cells. It may also play a role in ternary complex assembly of synaptic proteins at the postsynaptic membrane and coupling of signal transduction to membrane/cytoskeletal remodeling. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009] | CNK2, KSR2, MAGUIN, MRXSHG, connector enhancer of kinase suppressor of ras 2, CNK homolog protein 2, connector enhancer of KSR2, membrane-associated guanylate kinase-interacting protein |
CNOT4 | 2 | PTEN KO, VHL KO | 4,850 | CNOT4 | CCR4-NOT transcription complex subunit 4 | Homo sapiens (human) | The protein encoded by this gene is a subunit of the CCR4-NOT complex, a global transcriptional regulator. The encoded protein interacts with CNOT1 and has E3 ubiquitin ligase activity. Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2010] | CLONE243, NOT4, NOT4H, CCR4-associated factor 4, E3 ubiquitin-protein ligase CNOT4, NOT4 (negative regulator of transcription 4, yeast) homolog, RING-type E3 ubiquitin transferase CNOT4, potential transcriptional repressor NOT4Hp |
CTBP2 | 2 | KEAP1 KO, RB1 KO | 1,488 | CTBP2 | C-terminal binding protein 2 | Homo sapiens (human) | This gene produces alternative transcripts encoding two distinct proteins. One protein is a transcriptional repressor, while the other isoform is a major component of specialized synapses known as synaptic ribbons. Both proteins contain a NAD+ binding domain similar to NAD+-dependent 2-hydroxyacid dehydrogenases. A portion of the 3' untranslated region was used to map this gene to chromosome 21q21.3; however, it was noted that similar loci elsewhere in the genome are likely. Blast analysis shows that this gene is present on chromosome 10. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2014] | C-terminal-binding protein 2, ribeye |
DHODH | 2 | BAP1 KO, VHL KO | 1,723 | DHODH | dihydroorotate dehydrogenase (quinone) | Homo sapiens (human) | The protein encoded by this gene catalyzes the fourth enzymatic step, the ubiquinone-mediated oxidation of dihydroorotate to orotate, in de novo pyrimidine biosynthesis. This protein is a mitochondrial protein located on the outer surface of the inner mitochondrial membrane. [provided by RefSeq, Jul 2008] | DHOdehase, POADS, URA1, dihydroorotate dehydrogenase (quinone), mitochondrial, dihydroorotate oxidase, human complement of yeast URA1 |
DHX35 | 2 | LKB1 KO, VHL KO | 60,625 | DHX35 | DEAH-box helicase 35 | Homo sapiens (human) | DEAD box proteins characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The function of this gene product which is a member of this family, has not been determined. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2010] | C20orf15, DDX35, KAIA0875, probable ATP-dependent RNA helicase DHX35, DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35, DEAH (Asp-Glu-Ala-His) box polypeptide 35, DEAH-box protein 35 |
EBNA1BP2 | 2 | NF1 KO, RB1 KO | 10,969 | EBNA1BP2 | EBNA1 binding protein 2 | Homo sapiens (human) | null | EBP2, NOBP, P40, probable rRNA-processing protein EBP2, nuclear FGF3 binding protein, nucleolar protein p40, nucleolar protein p40; homolog of yeast EBNA1-binding protein |
ELMO2 | 2 | KEAP1 KO, RB1 KO | 63,916 | ELMO2 | engulfment and cell motility 2 | Homo sapiens (human) | The protein encoded by this gene interacts with the dedicator of cyto-kinesis 1 protein. Similarity to a C. elegans protein suggests that this protein may function in phagocytosis of apoptotic cells and in cell migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015] | CED-12, CED12, Ced-12A, ELMO-2, VMPI, engulfment and cell motility protein 2, PH domain protein CED12A, ced-12 homolog 2, protein ced-12 homolog A |
FBXO42 | 2 | LKB1 KO, VHL KO | 54,455 | FBXO42 | F-box protein 42 | Homo sapiens (human) | Members of the F-box protein family, such as FBXO42, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (SKP1A; MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Dec 2010] | Fbx42, JFK, F-box only protein 42, just one F-box and Kelch domain-containing protein |
G6PC | 2 | KEAP1 KO, NF1 KO | 2,538 | G6PC1 | glucose-6-phosphatase catalytic subunit 1 | Homo sapiens (human) | Glucose-6-phosphatase (G6Pase) is a multi-subunit integral membrane protein of the endoplasmic reticulum that is composed of a catalytic subunit and transporters for G6P, inorganic phosphate, and glucose. This gene (G6PC) is one of the three glucose-6-phosphatase catalytic-subunit-encoding genes in human: G6PC, G6PC2 and G6PC3. Glucose-6-phosphatase catalyzes the hydrolysis of D-glucose 6-phosphate to D-glucose and orthophosphate and is a key enzyme in glucose homeostasis, functioning in gluconeogenesis and glycogenolysis. Mutations in this gene cause glycogen storage disease type I (GSD1). This disease, also known as von Gierke disease, is a metabolic disorder characterized by severe hypoglycemia associated with the accumulation of glycogen and fat in the liver and kidneys.[provided by RefSeq, Feb 2011] | G6PC, G6PT, G6Pase, GSD1, GSD1a, G-6-Pase, G6Pase-alpha, glucose-6-phosphatase alpha |
GAK | 2 | RB1 KO, VHL KO | 2,580 | GAK | cyclin G associated kinase | Homo sapiens (human) | In all eukaryotes, the cell cycle is governed by cyclin-dependent protein kinases (CDKs), whose activities are regulated by cyclins and CDK inhibitors in a diverse array of mechanisms that involve the control of phosphorylation and dephosphorylation of Ser, Thr or Tyr residues. Cyclins are molecules that possess a consensus domain called the 'cyclin box.' In mammalian cells, 9 cyclin species have been identified, and they are referred to as cyclins A through I. Cyclin G is a direct transcriptional target of the p53 tumor suppressor gene product and thus functions downstream of p53. GAK is an association partner of cyclin G and CDK5. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015] | DNAJ26, DNAJC26, cyclin-G-associated kinase, auxilin-2, dnaJ homolog subfamily C member 26 |
GART | 2 | PBRM1 KO, RB1 KO | 2,618 | GART | phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase | Homo sapiens (human) | The protein encoded by this gene is a trifunctional polypeptide. It has phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase activity which is required for de novo purine biosynthesis. This enzyme is highly conserved in vertebrates. Alternative splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008] | AIRS, GARS, GARTF, PAIS, PGFT, PRGS, trifunctional purine biosynthetic protein adenosine-3, GAR transformylase, GARS-AIRS-GART, glycinamide ribonucleotide formyltransferase, glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase |
GTPBP2 | 2 | LKB1 KO, VHL KO | 54,676 | GTPBP2 | GTP binding protein 2 | Homo sapiens (human) | GTP-binding proteins, or G proteins, constitute a superfamily capable of binding GTP or GDP. G proteins are activated by binding GTP and are inactivated by hydrolyzing GTP to GDP. This general mechanism enables G proteins to perform a wide range of biologic activities.[supplied by OMIM, Jan 2003] | JABELS, GTP-binding protein 2 |
IGFALS | 2 | ARID1A KD, VHL KO | 3,483 | IGFALS | insulin like growth factor binding protein acid labile subunit | Homo sapiens (human) | The protein encoded by this gene is a serum protein that binds insulin-like growth factors, increasing their half-life and their vascular localization. Production of the encoded protein, which contains twenty leucine-rich repeats, is stimulated by growth hormone. Defects in this gene are a cause of acid-labile subunit deficiency, which maifests itself in a delayed and slow puberty. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Mar 2009] | ACLSD, ALS, insulin-like growth factor-binding protein complex acid labile subunit, insulin-like growth factor binding protein complex acid labile chain |
IKBKG | 2 | LKB1 KO, TP53BP1 KO | 8,517 | IKBKG | inhibitor of nuclear factor kappa B kinase regulatory subunit gamma | Homo sapiens (human) | This gene encodes the regulatory subunit of the inhibitor of kappaB kinase (IKK) complex, which activates NF-kappaB resulting in activation of genes involved in inflammation, immunity, cell survival, and other pathways. Mutations in this gene result in incontinentia pigmenti, hypohidrotic ectodermal dysplasia, and several other types of immunodeficiencies. A pseudogene highly similar to this locus is located in an adjacent region of the X chromosome. [provided by RefSeq, Mar 2016] | AMCBX1, EDAID1, FIP-3, FIP3, Fip3p, IKK-gamma, IKKAP1, IKKG, IMD33, IP, IP1, IP2, IPD2, NEMO, SAIDX, ZC2HC9, NF-kappa-B essential modulator, 14.7K (adenovirus E3 protein) interacting protein 3, I-kappa-B kinase subunit gamma, NF-kappa-B essential modifier, ikB kinase subunit gamma, ikB kinase-associated protein 1, incontinentia pigmenti, inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma, inhibitor of nuclear factor kappa B kinase subunit gamma |
JTB | 2 | LKB1 KO, NF1 KO | 10,899 | JTB | jumping translocation breakpoint | Homo sapiens (human) | null | HJTB, HSPC222, PAR, hJT, protein JTB, jumping translocation breakpoint protein, prostate androgen-regulated protein |
KIAA1524 | 2 | NF1 KO, VHL KO | 57,650 | CIP2A | cellular inhibitor of PP2A | Homo sapiens (human) | null | KIAA1524, NOCIVA, p90, protein CIP2A, cancerous inhibitor of PP2A, cancerous inhibitor of protein phosphatase 2A, cell proliferation regulating inhibitor of protein phosphatase 2A, p90 autoantigen |
KPNA4 | 2 | LKB1 KO, VHL KO | 3,840 | KPNA4 | karyopherin subunit alpha 4 | Homo sapiens (human) | The nuclear import of karyophilic proteins is directed by short amino acid sequences termed nuclear localization signals (NLSs). Karyopherins, or importins, are cytoplasmic proteins that recognize NLSs and dock NLS-containing proteins to the nuclear pore complex. The protein encoded by this gene shares the sequence similarity with Xenopus importin-alpha and Saccharomyces cerevisiae Srp1. This protein is found to interact with the NLSs of DNA helicase Q1 and SV40 T antigen. [provided by RefSeq, Jul 2008] | IPOA3, QIP1, SRP3, importin subunit alpha-3, importin alpha Q1, importin subunit alpha-4, karyopherin alpha 4 (importin alpha 3) |
MAPKAP1 | 2 | PBRM1 KO, TP53BP1 KO | 79,109 | MAPKAP1 | MAPK associated protein 1 | Homo sapiens (human) | This gene encodes a protein that is highly similar to the yeast SIN1 protein, a stress-activated protein kinase. Alternatively spliced transcript variants encoding distinct isoforms have been described. Alternate polyadenylation sites as well as alternate 3' UTRs have been identified for transcripts of this gene. [provided by RefSeq, Jul 2008] | JC310, MIP1, SIN1, SIN1b, SIN1g, target of rapamycin complex 2 subunit MAPKAP1, MEKK2-interacting protein 1, SAPK-interacting protein 1, TORC2 subunit MAPKAP1, mSIN1, mitogen-activated protein kinase 2-associated protein 1, mitogen-activated protein kinase associated protein 1, ras inhibitor MGC2745, stress-activated map kinase interacting protein 1, stress-activated protein kinase-interacting 1 |
MED13 | 2 | KEAP1 KO, RB1 KO | 9,969 | MED13 | mediator complex subunit 13 | Homo sapiens (human) | This gene encodes a component of the mediator complex (also known as TRAP, SMCC, DRIP, or ARC), a transcriptional coactivator complex thought to be required for the expression of almost all genes. The mediator complex is recruited by transcriptional activators or nuclear receptors to induce gene expression, possibly by interacting with RNA polymerase II and promoting the formation of a transcriptional pre-initiation complex. The product of this gene is proposed to form a sub-complex with MED12, cyclin C, and CDK8 that can negatively regulate transactivation by mediator. [provided by RefSeq, Jul 2008] | ARC250, DRIP250, HSPC221, MRD61, THRAP1, TRAP240, mediator of RNA polymerase II transcription subunit 13, activator-recruited cofactor 250 kDa component, mediator of RNA polymerase II transcription, subunit 13 homolog, thyroid hormone receptor-associated protein 1, thyroid hormone receptor-associated protein complex 240 kDa component, thyroid hormone receptor-associated protein complex component TRAP240, thyroid hormone receptor-associated protein, 240 kDa subunit, vitamin D3 receptor-interacting protein complex component DRIP250 |
MPV17 | 2 | LKB1 KO, VHL KO | 4,358 | MPV17 | mitochondrial inner membrane protein MPV17 | Homo sapiens (human) | This gene encodes a mitochondrial inner membrane protein that is implicated in the metabolism of reactive oxygen species. Mutations in this gene have been associated with the hepatocerebral form of mitochondrial DNA depletion syndrome (MDDS). [provided by RefSeq, Jul 2008] | CMT2EE, MTDPS6, SYM1, protein Mpv17, MPV17, mitochondrial inner membrane protein, MpV17 mitochondrial inner membrane protein, Mpv17, human homolog of glomerulosclerosis and nephrotic syndrome |
MTFMT | 2 | LKB1 KO, VHL KO | 123,263 | MTFMT | mitochondrial methionyl-tRNA formyltransferase | Homo sapiens (human) | The protein encoded by this nuclear gene localizes to the mitochondrion, where it catalyzes the formylation of methionyl-tRNA. [provided by RefSeq, Jun 2011] | COXPD15, FMT1, MC1DN27, methionyl-tRNA formyltransferase, mitochondrial |
NDUFB6 | 2 | LKB1 KO, NF1 KO | 4,712 | NDUFB6 | NADH:ubiquinone oxidoreductase subunit B6 | Homo sapiens (human) | The protein encoded by this gene is a subunit of the multisubunit NADH:ubiquinone oxidoreductase (complex I). Mammalian complex I is composed of 45 different subunits. It locates at the mitochondrial inner membrane. This protein has NADH dehydrogenase activity and oxidoreductase activity. It transfers electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Alternative splicing occurs at this locus and three transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jan 2011] | B17, CI, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6, CI-B17, NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa, NADH-ubiquinone oxidoreductase B17 subunit, NADH-ubiquinone oxidoreductase beta subunit, 6, complex I, mitochondrial respiratory chain, B17 subunit, complex I-B17 |
NUP160 | 2 | ARID1A KD, PBRM1 KO | 23,279 | NUP160 | nucleoporin 160 | Homo sapiens (human) | NUP160 is 1 of up to 60 proteins that make up the 120-MD nuclear pore complex, which mediates nucleoplasmic transport.[supplied by OMIM, Apr 2004] | NPHS19, nuclear pore complex protein Nup160, 160 kDa nucleoporin, nucleoporin 160kD, nucleoporin 160kDa, nucleoporin Nup160 |
PARD6B | 2 | PBRM1 KO, PTEN KO | 84,612 | PARD6B | par-6 family cell polarity regulator beta | Homo sapiens (human) | This gene is a member of the PAR6 family and encodes a protein with a PSD95/Discs-large/ZO1 (PDZ) domain, an OPR domain and a semi-Cdc42/Rac interactive binding (CRIB) domain. This cytoplasmic protein is involved in asymmetrical cell division and cell polarization processes as a member of a multi-protein complex. [provided by RefSeq, Jul 2008] | PAR6B, partitioning defective 6 homolog beta, PAR-6 beta, par-6 partitioning defective 6 homolog beta |
PDIA3 | 2 | PBRM1 KO, VHL KO | 2,923 | PDIA3 | protein disulfide isomerase family A member 3 | Homo sapiens (human) | This gene encodes a protein of the endoplasmic reticulum that interacts with lectin chaperones calreticulin and calnexin to modulate folding of newly synthesized glycoproteins. The protein was once thought to be a phospholipase; however, it has been demonstrated that the protein actually has protein disulfide isomerase activity. It is thought that complexes of lectins and this protein mediate protein folding by promoting formation of disulfide bonds in their glycoprotein substrates. This protein also functions as a molecular chaperone that prevents the formation of protein aggregates. [provided by RefSeq, Dec 2016] | ER60, ERp57, ERp60, ERp61, GRP57, GRP58, HEL-S-269, HEL-S-93n, HsT17083, P58, PI-PLC, protein disulfide-isomerase A3, 58 kDa glucose-regulated protein, 58 kDa microsomal protein, ER protein 57, ER protein 60, disulfide isomerase ER-60, endoplasmic reticulum P58, endoplasmic reticulum resident protein 57, endoplasmic reticulum resident protein 60, epididymis secretory protein Li 269, epididymis secretory sperm binding protein Li 93n, glucose regulated protein, 58kDa, phospholipase C-alpha, protein disulfide isomerase-associated 3 |
PDS5A | 2 | LKB1 KO, VHL KO | 23,244 | PDS5A | PDS5 cohesin associated factor A | Homo sapiens (human) | The protein encoded by this gene binds to the cohesin complex and associates with chromatin through most of the cell cycle. The encoded protein may play a role in regulating sister chromatid cohesion during mitosis. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010] | PIG54, SCC-112, SCC112, sister chromatid cohesion protein PDS5 homolog A, PDS5, regulator of cohesion maintenance, homolog A, cell proliferation-inducing gene 54 protein, sister chromatid cohesion protein 112 |
PIN1 | 2 | KEAP1 KO, RB1 KO | 5,300 | PIN1 | peptidylprolyl cis/trans isomerase, NIMA-interacting 1 | Homo sapiens (human) | Peptidyl-prolyl cis/trans isomerases (PPIases) catalyze the cis/trans isomerization of peptidyl-prolyl peptide bonds. This gene encodes one of the PPIases, which specifically binds to phosphorylated ser/thr-pro motifs to catalytically regulate the post-phosphorylation conformation of its substrates. The conformational regulation catalyzed by this PPIase has a profound impact on key proteins involved in the regulation of cell growth, genotoxic and other stress responses, the immune response, induction and maintenance of pluripotency, germ cell development, neuronal differentiation, and survival. This enzyme also plays a key role in the pathogenesis of Alzheimer's disease and many cancers. Multiple alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Jun 2011] | DOD, UBL5, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, PPIase Pin1, parvulin PIN1, protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1, protein interacting with never in mitosis A1, rotamase Pin1 |
PSMF1 | 2 | LKB1 KO, VHL KO | 9,491 | PSMF1 | proteasome inhibitor subunit 1 | Homo sapiens (human) | The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a protein that inhibits the activation of the proteasome by the 11S and 19S regulators. Alternative transcript variants have been identified for this gene. [provided by RefSeq, Jul 2008] | PI31, proteasome inhibitor PI31 subunit, proteasome (prosome, macropain) inhibitor subunit 1 (PI31) |
RAD54L | 2 | PTEN KO, VHL KO | 8,438 | RAD54L | RAD54 like | Homo sapiens (human) | The protein encoded by this gene belongs to the DEAD-like helicase superfamily, and shares similarity with Saccharomyces cerevisiae Rad54, a protein known to be involved in the homologous recombination and repair of DNA. This protein has been shown to play a role in homologous recombination related repair of DNA double-strand breaks. The binding of this protein to double-strand DNA induces a DNA topological change, which is thought to facilitate homologous DNA paring, and stimulate DNA recombination. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Dec 2008] | HR54, RAD54A, hHR54, hRAD54, DNA repair and recombination protein RAD54-like, RAD54 homolog |
RMI2 | 2 | CDH1 KO, TP53BP1 KO | 116,028 | RMI2 | RecQ mediated genome instability 2 | Homo sapiens (human) | RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008] | BLAP18, C16orf75, recQ-mediated genome instability protein 2, BLM-associated protein of 18 kDa, RMI2, RecQ mediated genome instability 2, homolog |
RRAS2 | 2 | BAP1 KO, KEAP1 KO | 22,800 | RRAS2 | RAS related 2 | Homo sapiens (human) | This gene encodes a member of the R-Ras subfamily of Ras-like small GTPases. The encoded protein associates with the plasma membrane and may function as a signal transducer. This protein may play an important role in activating signal transduction pathways that control cell proliferation. Mutations in this gene are associated with the growth of certain tumors. Pseudogenes of this gene are found on chromosomes 1 and 2. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2010] | NS12, TC21, ras-related protein R-Ras2, ras-like protein TC21, related RAS viral (r-ras) oncogene homolog 2, teratocarcinoma oncogene |
SDHD | 2 | BAP1 KO, VHL KO | 6,392 | SDHD | succinate dehydrogenase complex subunit D | Homo sapiens (human) | This gene encodes a member of complex II of the respiratory chain, which is responsible for the oxidation of succinate. The encoded protein is one of two integral membrane proteins anchoring the complex to the matrix side of the mitochondrial inner membrane. Mutations in this gene are associated with the formation of tumors, including hereditary paraganglioma. Transmission of disease occurs almost exclusively through the paternal allele, suggesting that this locus may be maternally imprinted. There are pseudogenes for this gene on chromosomes 1, 2, 3, 7, and 18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2013] | CBT1, CII-4, CWS3, MC2DN3, PGL, PGL1, PPGL1, QPs3, SDH4, cybS, succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial, malate dehydrogenase [quinone] cytochrome b small subunit, succinate dehydrogenase complex subunit D integral membrane protein, succinate-ubiquinone oxidoreductase cytochrome b small subunit, succinate-ubiquinone reductase membrane anchor subunit |
SHBG | 2 | KEAP1 KO, NF1 KO | 6,462 | SHBG | sex hormone binding globulin | Homo sapiens (human) | This gene encodes a steroid binding protein that was first described as a plasma protein secreted by the liver but is now thought to participate in the regulation of steroid responses. The encoded protein transports androgens and estrogens in the blood, binding each steroid molecule as a dimer formed from identical or nearly identical monomers. Polymorphisms in this gene have been associated with polycystic ovary syndrome and type 2 diabetes mellitus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014] | ABP, SBP, TEBG, sex hormone-binding globulin, sex steroid-binding protein, testis-specific androgen-binding protein, testosterone-binding beta-globulin, testosterone-estradiol-binding globulin, testosterone-estrogen-binding globulin |
STAC2 | 2 | KEAP1 KO, RB1 KO | 342,667 | STAC2 | SH3 and cysteine rich domain 2 | Homo sapiens (human) | This gene encodes a protein containing an SH3 domain and a zinc finger domain. The encoded protein has been shown to regulate calcium channel inactivation in a human cell line. Reduced expression of this gene has been observed in human heart failure. [provided by RefSeq, May 2017] | 24b2, 24b2/STAC2, SH3 and cysteine-rich domain-containing protein 2, SRC homology 3 and cysteine-rich domain-containing protein 2 |
STUB1 | 2 | BAP1 KO, NF1 KO | 10,273 | STUB1 | STIP1 homology and U-box containing protein 1 | Homo sapiens (human) | This gene encodes a protein containing tetratricopeptide repeat and a U-box that functions as a ubiquitin ligase/cochaperone. The encoded protein binds to and ubiquitinates shock cognate 71 kDa protein (Hspa8) and DNA polymerase beta (Polb), among other targets. Mutations in this gene cause spinocerebellar ataxia, autosomal recessive 16. Alternative splicing results in multiple transcript variants. There is a pseudogene for this gene on chromosome 2. [provided by RefSeq, Jun 2014] | CHIP, HSPABP2, NY-CO-7, SCA48, SCAR16, SDCCAG7, UBOX1, E3 ubiquitin-protein ligase CHIP, CLL-associated antigen KW-8, RING-type E3 ubiquitin transferase CHIP, STIP1 homology and U-box containing protein 1, E3 ubiquitin protein ligase, antigen NY-CO-7, carboxy terminus of Hsp70-interacting protein, heat shock protein A binding protein 2 (c-terminal), serologically defined colon cancer antigen 7 |
TADA1 | 2 | RB1 KO, TP53 KO | 117,143 | TADA1 | transcriptional adaptor 1 | Homo sapiens (human) | TADA1L is a protein subunit of the human STAGA complex (SPT3; (MIM 602947)/TAF9 (MIM 600822)/GCN5 (MIM 602301) acetyltransferase complex), which is a chromatin-modifying multiprotein complex (Martinez et al., 2001 [PubMed 11564863]).[supplied by OMIM, Apr 2009] | ADA1, HFI1, STAF42, TADA1L, hADA1, transcriptional adapter 1, SPT3-associated factor 42 (STAF42), transcriptional adapter 1-like protein, transcriptional adaptor 1 (HFI1 homolog, yeast) |
TMCO6 | 2 | KEAP1 KO, PTEN KO | 55,374 | TMCO6 | transmembrane and coiled-coil domains 6 | Homo sapiens (human) | null | PRO1580, transmembrane and coiled-coil domain-containing protein 6 |
DMAC1 | 2 | BAP1 KO, NF1 KO | 90,871 | DMAC1 | distal membrane arm assembly component 1 | Homo sapiens (human) | null | C9orf123, TMEM261, distal membrane-arm assembly complex protein 1, distal membrane arm assembly complex 1, transmembrane protein 261, transmembrane protein C9orf123 |
TOR4A | 2 | NF1 KO, VHL KO | 54,863 | TOR4A | torsin family 4 member A | Homo sapiens (human) | null | C9orf167, torsin-4A, torsin family protein C9orf167 |
TUSC2 | 2 | CDH1 KO, KEAP1 KO | 11,334 | TUSC2 | tumor suppressor 2, mitochondrial calcium regulator | Homo sapiens (human) | This gene is a highly conserved lung cancer candidate gene. No other information about this gene is currently available. [provided by RefSeq, Jul 2008] | C3orf11, FUS1, PAP, PDAP2, tumor suppressor candidate 2, PDGFA-associated protein 2, fus-1 protein, fusion 1 protein |
UNC13D | 2 | RB1 KO, TP53 KO | 201,294 | UNC13D | unc-13 homolog D | Homo sapiens (human) | This gene encodes a protein that is a member of the UNC13 family, containing similar domain structure as other family members but lacking an N-terminal phorbol ester-binding C1 domain present in other Munc13 proteins. The protein appears to play a role in vesicle maturation during exocytosis and is involved in regulation of cytolytic granules secretion. Mutations in this gene are associated with familial hemophagocytic lymphohistiocytosis type 3, a genetically heterogeneous, rare autosomal recessive disorder. [provided by RefSeq, Jul 2008] | FHL3, HLH3, HPLH3, Munc13-4, protein unc-13 homolog D |
USH1G | 2 | KEAP1 KO, NF1 KO | 124,590 | USH1G | USH1 protein network component sans | Homo sapiens (human) | This gene encodes a protein that contains three ankyrin domains, a class I PDZ-binding motif and a sterile alpha motif. The encoded protein interacts with harmonin, which is associated with Usher syndrome type 1C. This protein plays a role in the development and maintenance of the auditory and visual systems and functions in the cohesion of hair bundles formed by inner ear sensory cells. Mutations in this gene are associated with Usher syndrome type 1G (USH1G). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013] | ANKS4A, SANS, pre-mRNA splicing regulator USH1G, Usher syndrome 1G (autosomal recessive), scaffold protein containing ankyrin repeats and SAM domain, usher syndrome type-1G protein |
USP1 | 2 | PTEN KO, TP53BP1 KO | 7,398 | USP1 | ubiquitin specific peptidase 1 | Homo sapiens (human) | This gene encodes a member of the ubiquitin-specific processing (UBP) family of proteases that is a deubiquitinating enzyme (DUB) with His and Cys domains. This protein is located in the cytoplasm and cleaves the ubiquitin moiety from ubiquitin-fused precursors and ubiquitinylated proteins. The protein specifically deubiquitinates a protein in the Fanconi anemia (FA) DNA repair pathway. Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008] | UBP, ubiquitin carboxyl-terminal hydrolase 1, Ubiquitinyl hydrolase 1, Ubiquitin carboxyl-terminal hydrolase 1, ubiquitin thiolesterase 1, deubiquitinating enzyme 1, hUBP, ubiquitin specific processing protease 1, ubiquitin specific protease 1, ubiquitin thioesterase 1, ubiquitin thiolesterase 1 |
USP48 | 2 | NF1 KO, NF2 KO | 84,196 | USP48 | ubiquitin specific peptidase 48 | Homo sapiens (human) | This gene encodes a protein containing domains that associate it with the peptidase family C19, also known as family 2 of ubiquitin carboxyl-terminal hydrolases. Family members function as deubiquitinating enzymes, recognizing and hydrolyzing the peptide bond at the C-terminal glycine of ubiquitin. Enzymes in peptidase family C19 are involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008] | DFNA85, RAP1GA1, USP31, ubiquitin carboxyl-terminal hydrolase 48, deubiquitinating enzyme 48, ubiquitin specific protease 31, ubiquitin thioesterase 48, ubiquitin thiolesterase 48, ubiquitin-specific-processing protease 48 |
VGLL3 | 2 | KEAP1 KO, RB1 KO | 389,136 | VGLL3 | vestigial like family member 3 | Homo sapiens (human) | null | VGL-3, VGL3, transcription cofactor vestigial-like protein 3, colon carcinoma related protein |
WRAP53 | 2 | NF1 KO, TP53 KO | 55,135 | WRAP53 | WD repeat containing antisense to TP53 | Homo sapiens (human) | This gene encodes an essential component of the telomerase holoenzyme complex, a ribonucleoprotein complex required for telomere synthesis. This protein is enriched in Cajal bodies, nuclear sites of RNP processing that are important for telomerase function. It interacts with dyskerin, TERT and TERC, other components of active telomerase, and with small Cajal body RNAs (scaRNAs), which are involved in modifying splicing RNAs. This mRNA also functions as a p53 antisense transcript, that regulates endogenous p53 mRNA levels and further induction of p53 protein by targeting the 5' untranslated region of p53 mRNA. Alternatively spliced transcript variants which differ only in the 5' UTR have been found for this gene. [provided by RefSeq, Mar 2011] | DKCB3, TCAB1, WDR79, telomerase Cajal body protein 1, WD repeat-containing protein 79, WD repeat-containing protein WRAP53, WD40 protein Wrap53, WD40 repeat-containing protein antisense to TP53, WD40 repeat-containing protein encoding RNA antisense to p53, WRAP53beta |
YPEL5 | 2 | LKB1 KO, PBRM1 KO | 51,646 | YPEL5 | yippee like 5 | Homo sapiens (human) | null | CGI-127, protein yippee-like 5 |
Dataset Card for PMC_35559673_table_s datasets
Dataset Details
Dataset Description
This dataset contains the results of genome-wide CRISPR screens using isogenic knockout cells to uncover vulnerabilities in tumor suppressor-deficient cancer cells. The data were originally published by Feng et al., Sci. Adv. 8, eabm6638 (2022), and are available via PubMed Central (PMC). The supplementary tables included in this dataset provide detailed data on raw counts, essentiality calls, Bayes factors, and synthetic lethality (SL) hits. The dataset supports research into genetic dependencies and potential therapeutic targets.
- Curated by: Feng et al., Sci. Adv. 8, eabm6638 (2022)
- Funded by: Likely supported by institutions affiliated with the authors.
- Shared by: Feng et al.
- Language(s): Not applicable (biomedical dataset).
- License: CC BY 4.0
Dataset Sources
- Repository: PubMed Central
- Paper: Sci. Adv. 8, eabm6638 (2022)
- Supplementary Materials: Tables S1-S7
Dataset Structure
This dataset consists of seven tables (S1-S7), each representing a different aspect of the CRISPR screen results:
Table S1: Raw counts for all CRISPR screens in this study.
- File Mapping:
sciadv.abm6638_table_s1.xlsx
- File Mapping:
Table S2: Binary essentiality calls matrix.
- File Mapping:
sciadv.abm6638_table_s2.xlsx
- File Mapping:
Table S3: Quantile-normalized Bayes factor (QBF) matrix.
- File Mapping:
sciadv.abm6638_table_s3.xlsx
- File Mapping:
Table S5: Total SL hits identified for each TSG KO screen.
- File Mapping:
sciadv.abm6638_table_s5.xlsx
- File Mapping:
Table S6: Shared SL hits across each TSG KO screen.
- File Mapping:
sciadv.abm6638_table_s6.xlsx
- File Mapping:
Table S7: Unique SL hits for each TSG KO screen.
- File Mapping:
sciadv.abm6638_table_s7.xlsx
- File Mapping:
Dataset Creation
Curation Rationale
This dataset was curated to facilitate research into the vulnerabilities of cancer cells deficient in tumor suppressor genes. The binary essentiality calls, synthetic lethality (SL) hits, and other data allow researchers to explore genetic interactions that could serve as potential therapeutic targets. The methodology behind the CRISPR screens and SL hit identification was detailed by Feng et al. in their 2022 study.
Data Collection and Processing
Data were collected from genome-wide CRISPR screens performed on isogenic knockout cells. The data were processed to produce raw counts, binary essentiality calls, and genetic interaction matrices, including shared and unique synthetic lethal hits.
Relevant references describing the data processing and methods can be found in the following sources:
- Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens (PMID: 28655737)
- High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities (PMID: 26627737)
- Identifying chemogenetic interactions from CRISPR screens with drugZ (PMID: 31439014)
Who are the source data producers?
The data were produced by Feng et al., as part of their research published in Science Advances. The researchers were affiliated with academic institutions engaged in cancer genomics and CRISPR screening methodologies.
Annotations
Annotation Process
Annotations were primarily focused on identifying shared and unique synthetic lethality hits across tumor suppressor knockout screens. Automated processing tools like CRISPR analysis pipelines were employed for initial hit identification, followed by manual validation based on genetic interactions.
Who are the annotators?
The original authors, including experts in CRISPR screening and cancer genomics, performed the annotations. No third-party annotations were added.
Bias, Risks, and Limitations
The dataset is limited to specific cancer cell lines and tumor suppressor gene knockouts. As a result, the findings may not be generalizable across all cancer types. Users should exercise caution when interpreting results outside the experimental context.
Recommendations
Users should consult the references provided to better understand the experimental design and limitations. The dataset is best suited for research applications in cancer genomics, genetic interactions, and therapeutic target discovery.
Citation
BibTeX:
@article{
doi:10.1126/sciadv.abm6638,
author = {Xu Feng and Mengfan Tang and Merve Dede and Dan Su and Guangsheng Pei and Dadi Jiang and Chao Wang and Zhen Chen and Mi Li and Litong Nie and Yun Xiong and Siting Li and Jeong-Min Park and Huimin Zhang and Min Huang and Klaudia Szymonowicz and Zhongming Zhao and Traver Hart and Junjie Chen },
title = {Genome-wide CRISPR screens using isogenic cells reveal vulnerabilities conferred by loss of tumor suppressors},
journal = {Science Advances},
volume = {8},
number = {19},
pages = {eabm6638},
year = {2022},
doi = {10.1126/sciadv.abm6638},
URL = {https://www.science.org/doi/abs/10.1126/sciadv.abm6638},
eprint = {https://www.science.org/doi/pdf/10.1126/sciadv.abm6638},
abstract = {Exploiting cancer vulnerabilities is critical for the discovery of anticancer drugs. However, tumor suppressors cannot be directly targeted because of their loss of function. To uncover specific vulnerabilities for cells with deficiency in any given tumor suppressor(s), we performed genome-scale CRISPR loss-of-function screens using a panel of isogenic knockout cells we generated for 12 common tumor suppressors. Here, we provide a comprehensive and comparative dataset for genetic interactions between the whole-genome protein-coding genes and a panel of tumor suppressor genes, which allows us to uncover known and new high-confidence synthetic lethal interactions. Mining this dataset, we uncover essential paralog gene pairs, which could be a common mechanism for interpreting synthetic lethality. Moreover, we propose that some tumor suppressors could be targeted to suppress proliferation of cells with deficiency in other tumor suppressors. This dataset provides valuable information that can be further exploited for targeted cancer therapy. Whole-genome CRISPR screens uncover synthetic lethal interactions for tumor suppressors.}
}
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