Persius/hicric huggingface dataset:
SMN2
Survival of motor neuron 2 (SMN2) is a gene that encodes the SMN protein (full and truncated) in humans.

# Gene
The SMN2 gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. The telomeric (SMN1) and centromeric (SMN2) copies of this gene are nearly identical and encode the same protein. The critical sequence difference between the two genes is a single nucleotide in exon 7, which is thought to be an exon splice enhancer. The nucleotide substitution in SMN2 results in around 80-90% of its transcripts to be a truncated, unstable protein of no biological function (7SMN) and only 10-20% of its transcripts being full-length protein (fl-SMN).
Note that the nine exons of both the telomeric and centromeric copies are designated historically as exon 1, 2a, 2b, and 3-8. It is thought that gene conversion events may involve the two genes, leading to varying copy numbers of each gene.

# Clinical significance
While mutations in the telomeric copy are associated with spinal muscular atrophy, mutations in this gene, the centromeric copy, do not lead to disease. This gene may be a modifier of disease caused by mutation in the telomeric copy.
SNF8
Vacuolar-sorting protein SNF8 is a protein that in humans is encoded by the SNF8 gene.

# Model organisms
Model organisms have been used in the study of SNF8 function. A conditional knockout mouse line, called Snf8tm1a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty five tests were carried out on mutant mice and two significant abnormalities were observed.  No homozygous mutant embryos were identified during gestation, and therefore none survived until weaning. The remaining tests were carried out on heterozygous mutant adult mice; no additional significant abnormalities were observed in these animals.
SNX5
Sorting nexin-5 is a protein that in humans is encoded by the SNX5 gene.
This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein is a component of the mammalian retromer complex, which facilitates cargo retrieval from endosomes to the trans-Golgi network. It has also been shown to bind to the Fanconi anemia, complementation group A protein. This gene results in two transcript variants encoding the same protein.

# Model organisms
Model organisms have been used in the study of SNX5 function. A conditional knockout mouse line, called Snx5tm1a(KOMP)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists  at the Wellcome Trust Sanger Institute. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty five tests were carried out on homozygous mutant adult mice, however no significant abnormalities were observed.

# Interactions
SNX5 has been shown to interact with FANCA.
SNX9
Sorting nexin-9 is a protein that in humans is encoded by the SNX9 gene.
This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like some family members, but does contain an SH3 domain near its N-terminus. This protein interacts with the cytoplasmic domains of the precursor but not the processed forms of a disintegrin and metalloprotease domain 9 and 15. This protein binds the beta-appendage domain of adaptor protein 2 and may function to assist adaptor protein 2 in its role at the plasma membrane. This protein interacts with activated Cdc42-associated kinase-2 to regulate the degradation of epidermal growth factor receptor protein.

# Interactions
SNX9 has been shown to interact with ADAM9, DNM2 and ADAM15.
SOS1
Son of sevenless homolog 1 is a protein that in humans is encoded by the SOS1 gene.

# Function
RAS genes (e.g., MIM 190020) encode membrane-bound guanine nucleotide-binding proteins that function in the transduction of signals that control cell growth and differentiation. Binding of GTP activates RAS proteins, and subsequent hydrolysis of the bound GTP to GDP and phosphate inactivates signaling by these proteins. GTP binding can be catalyzed by guanine nucleotide exchange factors for RAS, and GTP hydrolysis can be accelerated by GTPase-activating proteins (GAPs). The first exchange factor to be identified for RAS was the S. cerevisiae CDC25 gene product. Genetic analysis indicated that CDC25 is essential for activation of RAS proteins. In Drosophila, the protein encoded by the 'son of sevenless' gene (Sos) contains a domain that shows sequence similarity with the catalytic domain of CDC25. Sos may act as a positive regulator of RAS by promoting guanine nucleotide exchange.

# Clinical significance
Recent studies also show that mutations in Sos1 can cause Noonan syndrome and hereditary gingival fibromatosis type 1. Noonan syndrome has also been shown to be caused by mutations in KRAS and PTPN11 genes. activators of the MAP kinase pathway.

# Interactions
SOS1 has been shown to interact with:
- ABI1,
- BCR gene,
- CRK,
- EPS8,
- Epidermal growth factor receptor,
- FRS2,
- Grb2,
- HRAS,
- ITSN1,
- MUC1,
- NCK1,
- PLCG1,
- PTPN11,
- SH3KBP1,  and
- SHC1. and
SOX4
Transcription factor SOX-4 is a protein that in humans is encoded by the SOX4 gene.

# Function
This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins, such as syndecan binding protein (syntenin). The protein may function in the apoptosis pathway leading to cell death as well as to tumorigenesis and may mediate downstream effects of parathyroid hormone (PTH) and PTH-related protein (PTHrP) in bone development. The solution structure has been resolved for the HMG-box of a similar mouse protein.
Sox4 is expressed in lymphocytes (B and T) and is required for B lymphocyte development.

# Clinical significance
A genomic region close to the SOX4 gene has been associated with endometrial cancer development.

# Interactions
SOX4 has been shown to interact with SDCBP.
SOX6
Transcription factor SOX-6 is a protein that in humans is encoded by the SOX6 gene.

# Function
The SOX gene family encodes a group of transcription factors defined by the conserved high mobility group (HMG) DNA-binding domain. Unlike most transcription factors, SOX transcription factors bind to the minor groove of DNA, causing a 70- to 85-degree bend and introducing local conformational changes.

# Interactions
SOX6 has been shown to interact with CTBP2 and CENPK.
It has also been demonstrated that SOX6 protein accumulates in the differentiating human erythrocytes, and then is able to downregulate its own transcription, by directly binding to an evolutionarily conserved consensus sequences located near SOX6 transcriptional start site.
Sox6 appears to have a crucial role in the transcriptional regulation of globin genes, and in directing the terminal differentiation of red blood cells.
SOX9
Transcription factor SOX-9 is a protein that in humans is encoded by the SOX9 gene.

# Function
SOX-9 recognizes the sequence CCTTGAG along with other members of the HMG-box class DNA-binding proteins. It acts during chondrocyte differentiation and, with steroidogenic factor 1, regulates transcription of the anti-Mullerian hormone (AMH) gene.
SOX-9 also plays a pivotal role in male sexual development; by working with Sf1, SOX-9 can produce AMH in Sertoli cells to inhibit the creation of a female reproductive system. It also interacts with a few other genes to promote the development of male sexual organs. The process starts when the transcription factor Testis determining factor (encoded by the sex-determining region SRY of the Y chromosome) activates SOX-9 activity by binding to an enhancer sequence upstream of the gene. Next, Sox9 activates FGF9 and forms feedforward loops with FGF9 and PGD2.  These loops are important for producing SOX-9; without these loops, SOX-9 would run out and the development of a female would almost certainly ensue. Activation of FGF9 by SOX-9 starts vital processes in male development, such as the creation of testis cords and the multiplication of Sertoli cells. The association of SOX-9 and Dax1 actually creates Sertoli cells, another vital process in male development.

# Clinical significance
Mutations lead to the skeletal malformation syndrome campomelic dysplasia, frequently with autosomal sex-reversal and cleft palate.
SOX9 sits in a gene desert on 17q24 in humans.  Deletions, disruptions by translocation breakpoints and a single point mutation of highly conserved non-coding elements located > 1 Mb from the transcription unit on either side of SOX9 have been associated with Pierre Robin Sequence, often with a cleft palate.

## Role in sex reversal
Mutations in Sox9 or any associated genes can cause reversal of sex and hermaphroditism (or intersexuality in humans). If Fgf9, which is activated by Sox9, is not present, a fetus with both X and Y chromosomes can develop female gonads; the same is true if Dax1 is not present. The related phenomena of hermaphroditism can be caused by unusual activity of the SRY, usually when it's translocated onto the X-chromosome and its activity is only activated in some cells.

# Interactions
SOX9 has been shown to interact with Steroidogenic factor 1, MED12 and MAF.
SPEN
Msx2-interacting protein is a protein that in humans is encoded by the SPEN gene.
This gene encodes a hormone inducible transcriptional repressor. Repression of transcription by this gene product can occur through interactions with other repressors, by the recruitment of proteins involved in histone deacetylation, or through sequestration of transcriptional activators. The product of this gene contains a carboxy-terminal domain that permits binding to other corepressor proteins. This domain also permits interaction with members of the NuRD complex, a nucleosome remodeling protein complex that contains deacetylase activity. In addition, this repressor contains several RNA recognition motifs that confer binding to a steroid receptor RNA coactivator; this binding can modulate the activity of both liganded and nonliganded steroid receptors.

# Interactions
SPEN has been shown to interact with HDAC1, SRA1 and Nuclear receptor co-repressor 2.
SPI1
Transcription factor PU.1 is a protein that in humans is encoded by the SPI1 gene.

# Function
This gene encodes an ETS-domain transcription factor that activates gene expression during myeloid and B-lymphoid cell development. The nuclear protein binds to a purine-rich sequence known as the PU-box found on enhancers of target genes, and regulates their expression in coordination with other transcription factors and cofactors. The protein can also regulate alternative splicing of target genes. Multiple transcript variants encoding different isoforms have been found for this gene.

# Structure
The ETS domain is the DNA-binding module of PU.1 and other ETS-family transcription factors.

# Interactions
SPI1 has been shown to interact with:
- FUS,
- GATA2,
- IRF4, and
- NONO.
SPOP
Speckle-type POZ protein is a protein that in humans is encoded by the SPOP gene.
This gene encodes a protein that may modulate the transcriptional repression activities of death-associated protein 6 (DAXX), which interacts with histone deacetylase, core histones, and other histone-associated proteins. In mouse, the encoded protein binds to the putative leucine zipper domain of macroH2A1.2, a variant H2A histone that is enriched on inactivated X chromosomes. The BTB/POZ domain of this protein has been shown in other proteins to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes. Alternative splicing of this gene results in multiple transcript variants encoding the same protein.

# Clinical relevance
Mutations in SPOP lead to a type of prostate tumor thought to be involved in about 15% of all prostate cancers.
SRA1
Steroid receptor RNA activator 1 also known as steroid receptor RNA activator protein (SRAP) is a protein that in humans is encoded by the SRA1 gene.  The mRNA transcribed from the SRA1 gene is a component of the ribonucleoprotein complex containing NCOA1. This functional RNA also encodes a protein.

# Function
This gene is involved in transcriptional coactivation by steroid receptor. There is currently data suggesting this gene encodes both a non-coding RNA that functions as part of a ribonucleoprotein complex and a protein coding mRNA. Increased expression of both the transcript and the protein is associated with cancer.

# Interactions
SRA1 has been shown to interact with:
- Estrogen receptor alpha,
- DDX17,
- Nuclear receptor coactivator 2, and
- SPEN.
The SRAP has been shown to interact with its SRA RNA counterpart indirectly with the functional sub-structure STR7 of SRA RNA.  Originally proposed to be RRM containing, SRAP has been demonstrated to have a helix bundle at its C-terminal end while N-terminal to this domain appears unstructured.
SS18
Protein SSXT is a protein that in humans is encoded by the SS18 gene.

# Function
SS18 is a member of the human SWI/SNF chromatin remodeling complex.

# Clinical significance
SS18 is involved in a chromosomal translocation commonly found in synovial sarcoma.

# Interactions
SS18 has been shown to interact with:
- EP300,
- MLLT10,
- SMARCA2, and
- SMARCB1.
SSX6
SSX family member 6, pseudogene is a protein that in humans is encoded by the SSX6 gene.

# Function
This gene belongs to the family of highly homologous synovial sarcoma X (SSX) breakpoint proteins. These proteins may function as transcriptional repressors. They are also capable of eliciting spontaneously humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy.
SSX1, SSX2, and SSX4 genes have been involved in the t(X;18) translocation characteristically found in all synovial sarcomas. This gene is classified as a pseudogene because a splice donor in the 3' UTR has changed compared to other family members, rendering the transcript a candidate for nonsense-mediated mRNA decay (NMD). .
ST14
Suppressor of tumorigenicity 14 protein, also known as matriptase, is a protein that in humans is encoded by the ST14 gene. ST14 orthologs have been identified in most mammals for which complete genome data are available.

# Function
Matriptase is an epithelial-derived, integral membrane serine protease. This protease forms a complex with the Kunitz-type serine protease inhibitor, HAI-1, and is found to be activated by sphingosine-1-phosphate. This protease has been shown to cleave and activate hepatocyte growth factor/scatter factor, and urokinase plasminogen activator, which suggest the function of this protease as an epithelial membrane activator for other proteases and latent growth factors.
Matriptase is a type II transmembrane serine protease expressed in most human epithelia, where it is coexpressed with its cognate transmembrane inhibitor, hepatocyte growth factor activator inhibitor (HAI)-1. Activation of the matriptase zymogen requires sequential N-terminal cleavage, activation site autocleavage, and transient association with HAI-1. Matriptase has an essential physiological role in profilaggrin processing, corneocyte maturation, and lipid matrix formation associated with terminal differentiation of the oral epithelium and the epidermis, and is also critical for hair follicle growth.  Matriptase is an 80- to 90-kDa cell surface glycoprotein with a complex modular structure that is common to all matriptases.

# Clinical significance
The expression of this protease has been associated with breast, colon, prostate, and ovarian tumors, which implicates its role in cancer invasion, and metastasis.
Matriptase and HAI expression are frequently dysregulated in human cancer, and matriptase expression that is unopposed by HAI-1 potently promotes carcinogenesis and metastatic dissemination in animal models.
STIL
SCL-interrupting locus protein is a protein that in humans is encoded by the STIL gene.
This gene encodes a cytoplasmic protein implicated in regulation of the mitotic spindle checkpoint, a regulatory pathway that monitors chromosome segregation during cell division to ensure the proper distribution of chromosomes to daughter cells. The protein is phosphorylated in mitosis and in response to activation of the spindle checkpoint, and disappears when cells transition to G1 phase. It interacts with a mitotic regulator, and its expression is required to efficiently activate the spindle checkpoint. It is proposed to regulate Cdc2 kinase activity during spindle checkpoint arrest. Chromosomal deletions that fuse this gene and the adjacent locus commonly occur in T cell leukemias, and are thought to arise through illegitimate recombination events. Multiple transcript variants encoding different isoforms have been found for this gene.
Homozygous mutations in the STIL gene cause primary microcephaly (small brain) in humans.
STK4
Serine/threonine-protein kinase 4 is an enzyme that in humans is encoded by the STK4 gene.

# Function
The protein encoded by this gene is a cytoplasmic kinase that is structurally similar to the yeast Ste20p (sterile 20 protein) kinase, which acts upstream of the stress-induced mitogen-activated protein kinase (MAPK) cascade. The encoded protein can phosphorylate myelin basic protein and undergoes autophosphorylation. A caspase-cleaved fragment of the encoded protein has been shown to be capable of phosphorylating histone H2B. The particular phosphorylation catalyzed by this protein has been correlated with apoptosis, and it's possible that this protein induces the chromatin condensation observed in this process.

# Interactions
STK4 has been shown to interact with PRKRIR.
STK4 has also been shown to prevent, through Yap1 coactivator modulation, haematological tumor cell apoptosis.
STX2
Syntaxin-2, also known as epimorphin, is a protein that in humans is encoded by the STX2 gene.
The product of this gene belongs to the syntaxin/epimorphin family of proteins. The syntaxins are a large protein family implicated in the targeting and fusion of intracellular transport vesicles. The product of this gene regulates epithelial-mesenchymal interactions and epithelial cell morphogenesis and activation. Alternatively spliced transcript variants encoding different isoforms have been identified. When the N terminus is on the cytosolic face it acts as a t-SNARE involved in intracellular vesicle docking and is called  Syntaxin-2. When flipped inside out, i.e. N terminus hangs out on the extracellular surface (by some nonclassical secretion pathway) it acts as a versatile morphogen and is called epimorphin. This membrane protein enjoys the double choice of another form of topological alternatives of being targeted to either apical or basolateral surface of an epithelial cell in a regulated way depending on various contexts. When expressed by mesenchymal cells it can instruct epithelial morphogenesis at epithelial mesenchymal interfaces.

# Interactions
STX2 has been shown to interact with SNAP-25, SNAP23, STXBP1 and Syntaxin binding protein 3.
STX7
Syntaxin-7 is a protein that in humans is encoded by the STX7 gene.
In melanocytic cells STX7 gene expression may be regulated by MITF.

# Interactions
STX7 has been shown to interact with STX8, VPS18, Vesicle-associated membrane protein 8 and VPS11.
STX8
Syntaxin-8 is a protein that in humans is encoded by the STX8 gene.
Syntaxin 8 directly interacts with HECTd3 and has similar subcellular localization. The protein has been shown to form the SNARE complex with syntaxin 7, vti1b and endobrevin. These function as the machinery for the homotypic fusion of late endosomes.

# Model organisms
Model organisms have been used in the study of STX8 function. A conditional knockout mouse line, called Stx8tm2a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium programa high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientistsat the Wellcome Trust Sanger Institute. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty four tests were carried out on homozygous mutant adult mice, however no significant abnormalities were observed.

# Interactions
STX8 has been shown to interact with Vesicle-associated membrane protein 8, VTI1B and STX7.
SUFU
Suppressor of fused homolog is a protein that in humans is encoded by the SUFU gene.

# Function
SUFU encodes a component of the sonic hedgehog (SHH) / patched (PTCH) signaling pathway. Mutations in genes encoding components of this pathway are deleterious for normal development and are associated with cancer-predisposing syndromes (e.g., holoprosencephaly, HPE3; basal cell nevus syndrome, BCNS; and Greig cephalopolysyndactyly syndrome; GCPS).

# Interactions
SUFU has been shown to interact with GLI1, GLI3 and PEX26.
SYT1
Synaptotagmin-1 is a protein that in humans is encoded by the SYT1 gene.

# Function
The synaptotagmins are integral membrane proteins of synaptic vesicles thought to serve as sensors for calcium ions (Ca2+)in the process of vesicular trafficking and exocytosis. Calcium ion binding to synaptotagmin I participates in triggering neurotransmitter release at the synapse (Fernandez-Chacon et al., 2001). 
SYT1 is the master switch responsible for allowing the human brain to release neurotransmitters. SYT1 senses calcium ion concentrations as low as 10 ppm and subsequently signals the SNARE complex to open fusion pores.

# Interactions
SYT1 has been shown to interact with SNAP-25, STX1A and S100A13.
SZT2
Seizure threshold 2 homolog is a protein that in humans is encoded by the SZT2 gene.

# Function
The protein encoded by this gene is expressed in the brain, predominantly in the parietal and frontal cortex as well as in dorsal root ganglia. It is localized to the peroxisome, and is implicated in resistance to oxidative stress. It likely functions by increasing superoxide dismutase (SOD) activity, but itself has no direct SOD activity. Studies in mice show that this gene confers low seizure threshold, and may also enhance epileptogenesis.

# Clinical significance
Mutations in this gene have been shown to cause infantile encephalopathy with epilepsy and dysmorphic corpus callosum.