# TMEM202

Transmembrane 202 protein (Homo sapiens, TMEM202) is encoded by the gene TMEM202 and is a member of the Claudin2 superfamily. Human paralogs include LIMP2, GSG1, CLDND2, NKG7. The specific function of TMEM202 has largely yet to be elucidated, but other Claudin2 superfamily proteins plays important roles in paracellular transport by contributing to the structure of gap junctions. In S. scrofa (wild boar), TMEM202 has been found to aid in sperm motility, fertilization, and spermatogenesis.

## Gene
### Location

The TMEM202 gene spans 10,063 nucleotides on chromosome 15 located at 15q23-q24.1 and on the forward strand. The most complete isoform of TMEM202 (transcript variant 1) contains five exons. The genetic neighborhood is rather scarce, as HEXA is the gene nearest to TMEM202 and is found ~23,000 nucleotides upstream.

### Expression

TMEM202 demonstrates restricted and low expression in H. sapiens testis.

## RNA and Transcriptional variants

There exist four transcriptional variants of TMEM202 mRNA.
Properties of TMEM202 mRNA Transcript Variants. :
| TMEM202 Transcript Variant | Accession Number | mRNA length (nucleotides) | 5'UTR length (nucleotides) | Exon 1 | Exon 2 | Exon 3 | Exon 4 | Exon 5 |
| Transcript variant 1 | NM_001080462 | 1318 | 22 | Y | Y | Y | Y | Y |
| Isoform X1 | XM_011521497 | 1326 | 147 | X | * | Y | Y | Y |
| Isoform X2 | XM_024449910 | 1186 | 22 | Y | Y | Y | X | Y |
| Isoform X3 | XM_011521499 | 1132 | 169 | X | X | Y | Y | Y |
'Y' indicates the presence of the exon in the specific transcript variant, whereas 'X' denotes absence of the exon. '*' represents partial loss of exon two in isoform X1 (first thirty-six nucleotides).

## TMEM202 protein

TMEM202 is classified as a multi-pass protein as it consists of four transmembrane domains with helical structure (residue: 53-75, 121-141, 155-175, and 189-209) and one disordered region (242-273). TMEM202 protein is a member of the Claudin2 superfamily. Claudin proteins often form protein-protein interactions in epithelial and endothelial tissue, contributing to the scaffolding of the tight junction.
Properties of TMEM202 Protein Variants. :
| TMEM202 Protein Variant | Accession Number | Protein Length (A.A) | Approx. Molecular Weight Prior to PTMs (kDa) | Exons present | Similarity (%) | Internal Composition |
| TMEM202 Variant 1 | NP_001073931.1 | 273 | ~31.2 | 1-5 | 100 | L: (+) W: (+) |
| TMEM202 Isoform X1 | XP_011519799.1 | 234 | ~26.8 | Part of 2; 3-5 | 85.7 | L: (+) W: (++) |
| TMEM202 Isoform X2 | XP_024305678.1 | 229 | ~26.1 | 1-3, 5 | 83.9 | W: (+) A: (-) D: (-) |
| TMEM202 Isoform X3 | XP_011519801.1 | 162 | ~18.5 | 3-5 | 58.6 | N/A |
Similarity was calculated using Pairwise Sequence Alignments (PSAs) where all transcripts were aligned to transcript variant 1. The approximate molecular weight was calculated prior to post-translational modifications (PTMs), such as cleavages in the sequence or binding of additional molecules (e.g., phosphorylation, n-glycosylation). Emboss SAPS was used to determine relative composition of residues as compared to their database of H. sapiens samples. One (+/-) denotes one standard deviation away from the average, whereas two (++/--) indicate two standard deviations away from the average. Proteins with a (+/-) can be classified as rich or poor for that amino acid (e.g., TMEM202 Variant 1 is leucine- and tryptophan-rich).

### TMEM202 Secondary Structure

The figure to the right, TMEM202 Secondary Domains shows the predicted secondary structure of TMEM202, along with exon boundaries.

## Gene Level Regulation
### Expression pattern

The expression of TMEM202 was found to be restricted to the testis during a RNA-sequence study of normal adult human tissue (27 different tissues were analyzed from 95 individual human samples; RPKM = ~5). An additional RNA-seq study of human fetal tissue (six tissue types were sequenced from 35 human fetal samples between 10 and 20 weeks gestational time) found that TMEM202 is present in intestinal, lung, and stomach tissues at week 10 of gestation and in adrenal tissue at week 20.

### Promoter region and transcription factor binding

The figure Annotated Promoter Sequence of Human TMEM202 shows potential binding locations for the most compatible transcription factors. The promoter region was defined as the 500 nucleotides directly upstream of transcription (denoted by a right pointing arrow).
TMEM202 Transcription Factors Potentially Binding in Promoter Region.
| Transcription Factors Name | Binding Site Location (Bases upstream - Strand) | Binding Score | Function of Transcription Factor | Reason for Identification |
| NFIC | 1 - Minus | 421 | Individually capable of activating transcription | Function; proximity to start codon; high conservation |
| ZSCAN4 (Twice) | 49 - Minus 134 - Plus | 461 609 | Regulates embryonic stem cell pluripotency | Function relates to microarray studies; high binding score; appears twice in the promoter region |
| ZBTB24 | 75 - Minus | 554 | Involved in BMP2-induced transcription* | High binding score |
| TBP | 106 - Plus | 421 | Aids in the initiation of RNA polymerase II-dependent transcription | Function; high conservation |
| DUXA (Twice) | 109 - Plus 109 - Minus | 476 476 | Acts as a repressor | Function; binding sites on both the plus and minus strand at the same location; overlapping binding sequence with Tfcp2l1; appears twice in the promoter region |
| Tfcp2l1 | 115 - Plus | 446 | Facilitates establishment and maintenance of pluripotency in embryonic stem cells | Function relates to microarray studies; overlapping binding sequence with DUXA, ELF3 |
| ELF3 | 122 - Plus | 400 | Acts as an activator | Function; overlapping binding sequence with Tfcp2l1 |
| TBX20 | 124 - Minus | 449 | Acts as a transcriptional activator and repressor | Function; overlapping binding sequence with EOMES |
| EOMES | 125 - Minus | 418 | Acts as transcriptional activator playing a crucial role during development | Function; overlapping binding sequence with TBX20 |
| Prdm5 | 148 - Minus | 427 | Acts a transcriptional repressor | Function |
| MEIS2 | 178 - Plus | 405 | Transcriptional regulation - stabilization of the homeoprotein-DNA complex | Function; overlapping binding sequence with FOXH1; moderate coservation |
| FOXH1 | 182 - Minus | 481 | Acts as an activator | Function; overlapping binding sequence with MEIS2; moderate conservation |
| KLF9 | 205 - Plus | 403 | Selectively activates transcription when bound to GC box promoter elements | Function; overlapping binding sequence with NR1D1 |
| NR1D1 | 205 - Minus | 405 | Acts a transcriptional repressor | Function; overlapping binding sequence with KLF9 |
| Sox11 | 221 - Plus | 421 | Acts as an activator | Function; high coservation |
| ONECUT3 | 245 - Minus | 508 | Acts as an activator | Function; high binding score; overlapping binding sequence with ONECUT1 |
| ONECUT1 | 247 - Minus | 346 | Acts as an activator | Function; overlapping binding sequence with ONECUT3; moderate conservation |
| FOXD3 (Twice) | 270 - Minus 364 - Minus | 446 467 | Acts as a transcriptional activator and repressor | Function; appears twice in the promoter region; overlapping binding sequence with HOXB13; high conservation |
| HOXB13 | 355 - Plus | 450 | Involved in the developmental regulatory system provides cells with positional identities along the anterior-posterior axis | Function; overlapping binding sequence with FOXD3 |
| Neurod2 | 395 - Minus | 403 | Involved in neuronal determination | Function |
(*) Indicates hypothesized function. A higher binding score suggests a higher likelihood that the transcription factor will bind to the sequence when present—binding scores were calculated by the Jaspar Database. This is a non-exhaustive list of potential transcription factors that may bind to TMEM202, but presents transcription factors with the highest binding score or potentially illuminating qualities within the 500 base promoter region.

## Protein level regulation
### Post-translational modifications

Predicted Post-Translational Modifications of TMEM202.
| Type of PTM | Number of Sites | Location | Source | Notes |
| Generic phosphorylation | 29 | S13, S39, S254 | NetPhos | Locations denoted were three highest scored |
| Phosphorylation | 2 | Y25, S245 | PhosphoPlus | |
| GlcNAc O-glycosylation | 2 | T107, S245 | DictyOGlyc | |
| N-myristoylation | 2 | G61, G145 | MyHit | |
| Acetylation | 1 | K264 | PhosphoPlus | |
| N-linked glycosylation | 1 | N225 | NetNGlyc | |
| N-linked glycosylation | 1 | N225 | ELM | |
| Arginine and lysine propeptide cleavage sites | None | None | ProP | |
| C-mannosylation sites | None | None | NetCGlyc | |
| GPI Anchors | None | None | NetGPI | Likelihood not anchored by GPI - 0.993 |
| O-GalNAc (mucin type) glycosylation sites | None | None | NetOGlyc | |
Different types of PTM’s were predicted using a variety of computational systems. Locations bolded were predicted by two or more unique systems.

## TMEM202 homology and evolution
### Paralogs of TMEM202

Four paralogs, LIMP2, GSG1, CLDND2, NKG7, have been discovered for TMEM202 and are outlined in the table below.
Paralogs of H. sapiens TMEM202.
| TMEM202 Paralogs | Genus and Species | Name | Common Name | Accession Number | Sequence Length (amino acids) | Sequence Identity to Human Protein (%) | Sequence Similarity to Human Protein (%) | Sequence Divergence (n) | Corrected Sequence Divergence (m) |
| Protein of Interest | Homo sapiens | Transmembrane Protein 202 | TMEM202 | NP_001073931.1 | 273 | 100 | 100 | 0 | 0 |
| Paralogs | Homo sapiens | Lens fiber membrane intrinsic protein isoform 2 | LIMP2 | NP_085915.2 | 215 | 14.5 | 28.6 | 85.5 | 193.1021537 |
| | Homo sapiens | Protein NKG7 isoform 1 | NKG7 | NP_005592.1 | 165 | 14.3 | 27.9 | 85.7 | 194.4910649 |
| | Homo sapiens | Claudin domain-containing protein 2 | CLDND2 | NP_689566.1 | 167 | 14.2 | 25.4 | 85.8 | 195.1928221 |
| | Homo sapiens | Germ cell-specific gene 1 protein isoform 1 | GSG1 | NP_112579.2 | 285 | 8.5 | 15.3 | 91.5 | 246.5104022 |
Sequences characterized as paralogs were aligned to TMEM202 via pairwise analysis (PSA). The results of the PSA gave percent identity and similarity values, which were also used to calculate the sequence divergence value (n) and corrected sequence divergence value (m). Estimated median date of divergence is based on predicted values found on TimeTree.

### Orthologs of TMEM202

Orthologs were found using the NCBI Blast database by searching for proteins with similar sequences to the H. sapiens TMEM202 protein. All taxia with sequenced proteins, including bacteria, fungi and plants were searched; however, bony fish were found to be the most diverged species to have orthologous proteins. Orthologs were also found in amphibians, birds, reptiles, and mammals. Orthologs are characterized in the table below:
Orthologs of H. sapiens TMEM202.
| TMEM202 | Taxonomic Group | Genus and Species | Common Name | Accession Number | Median Date of Divergence (MYA) | Sequence Length (amino acids) | Sequence Identity to Human Protein (%) | Sequence Similarity to Human Protein (%) | Sequence Divergence (n) | Corrected Sequence Divergence (m) |
| Mammals | Primates | Homo sapiens | Human | NP_001073931.1 | 0 | 273 | 100.0 | 100.0 | 0.0 | 0.0 |
| | Lagomorphs | Ochotona princeps | American pika | XP_004594772 | 87 | 263 | 58.3 | 71.4 | 41.7 | 54.0 |
| | Perissodactyla | Diceros bicornis minor | South-central black rhinoceros | XP_058396452.1 | 94 | 271 | 76.6 | 82.4 | 23.4 | 26.7 |
| | Artiodactyls | Sus scrofa | Wild boar | XP_005666231.1 | 94 | 271 | 68.9 | 79.1 | 31.1 | 37.3 |
| | Chiroptera | Rousettus aegyptiacus | Egyptian fruit bat | XP_015982472.2 | 94 | 289 | 63.7 | 75.8 | 36.3 | 45.1 |
| | Eulipotyphla | Condylura cristata | Star-nosed mole | XP_004687557.1 | 94 | 267 | 61.7 | 73.7 | 38.3 | 48.3 |
| | Proboscideans | Elephas maximus indicus | Indian elephant | XP_049761646.1 | 99 | 266 | 73.6 | 82.1 | 26.4 | 30.7 |
| | Diprotodontia | Vombatus ursinus | Common wombat | XP_027713789.1 | 160 | 288 | 42.6 | 55.1 | 57.4 | 85.3 |
| | Carnivorous marsupials | Sarcophilus harrisii | Tasmanian devil | XP_031812217.1 | 160 | 324 | 38.4 | 50.8 | 61.6 | 95.7 |
| Reptilia | Testudines | Chelydra serpentina | Common snapping turtle | KAG6921653.1 | 319 | 190 | 18.3 | 33.1 | 81.7 | 169.8 |
| | Squamata | Podarcis lilfordi | Lilford's wall lizard | CAI5781213.1 | 319 | 193 | 18.0 | 32.5 | 82.0 | 171.5 |
| | Squamata | Naja naja | Indian cobra | KAG8143384.1 | 319 | 150 | 17.0 | 27.8 | 83.0 | 177.2 |
| | Testudines | Chrysemys picta bellii | Painted turtle | XP_065430698.1 | 319 | 484 | 12.5 | 20.5 | 87.5 | 207.9 |
| Aves | Psittaciformes | Strigops habroptila | Kākāpō | XP_030329880.1 | 319 | 320 | 14.2 | 20.3 | 85.8 | 195.2 |
| | Gruiformes | Grus japonensis | Red-crowned crane | GAB0205531.1 | 319 | 238 | 11.3 | 19.8 | 88.7 | 218.0 |
| | Passeriformes | Pseudopodoces humilis | Ground tit | XP_005533382 | 319 | 641 | 7.7 | 11.2 | 92.3 | 256.4 |
| Amphibia | Anura | Eleutherodactylus coqui | Common coquí | XP_066461729.1 | 352 | 192 | 20.1 | 31.9 | 79.9 | 160.4 |
| | Anura | Ascaphus truei | Coastal tailed frog | MEE6481875.1 | 352 | 168 | 15.7 | 27.2 | 84.3 | 185.2 |
| | Urodela | Pleurodeles waltl | Iberian ribbed newt | KAJ1132505.1 | 352 | 179 | 14.9 | 28.4 | 85.1 | 190.4 |
| Vertebrata | Cypriniformes | Cyprinus carpio | Common carp | KTG06534.1 | 429 | 224 | 15.8 | 30.6 | 84.2 | 184.5 |
| | Notacanthiformes | Aldrovandia affinis | Gilbert's halosaurid fish | KAJ8399001.1 | 429 | 173 | 14.2 | 28.4 | 85.8 | 195.2 |
Sequences characterized as orthologs were aligned to TMEM202 via pairwise analysis (PSA). The results of the PSA gave percent identity and similarity values, which were also used to calculate the sequence divergence value (n) and corrected sequence divergence value (m). Estimated median date of divergence is based on predicted values found on TimeTree.

### Evolution of TMEM202

The evolutionary history of TMEM202 appears to have begun approximately 429 years ago as orthologs of the protein were found in species of bony fish. Since then, TMEM202 has evolved in species of amphibians, reptiles, birds, and mammals. This evolution is quantified in Evolutionary History of TMEM202 compared to Fibrinogen a, cyctochrome C, where corrected sequence divergence of TMEM202 orthologs was graphed over time in comparison to fibrinogen a and cytochrome c.

#### Evolutionary History of TMEM202 compared to fibrinogen a, cytochrome C.

Fibrinogen alpha (a) is a fast-evolving protein as compared to cytochrome c, a slow-evolving protein. Across its evolution, TMEM202 has undergone numerous amino acid mutations, as it has ascertained mutations at a similar rate to fibrinogen alpha. For this reason, TMEM202 can be considered a fast-evolving protein.
To the left, Unrooted Phylogenetic Tree of Homo sapiens TMEM202 and its Orthologous Species, helps visualize divergence of some orthologs from humans. Species were further classified into mammals, aves, amphibians, and reptiles.

## TMEM202 interacting proteins

STRING Network revealed proteins found to interact with TMEM202 and are detailed in the table below. Along with those proteins, are kinases predicted to phosphorylate TMEM202.

### Proteins predicted to interact with TMEM202

| Protein Abbreviation | Protein Name | Basis of Identification | Function | Notes |
| SPATA31D1 | Spermatogenesis-associated protein 31D1 | STRING Network | Might be involved in cell differentiation and spermatogenesis | Predicted to be a part of the cell membrane |
| CFAP45 | Cilia and flagella associated protein 45 | STRING Network | Enables AMP binding and is involved in establishing left/right asymmetry of the flagella | |
| SPACA1 | Sperm acrosome membrane-associated protein 1 | STRING Network | Aids in the acrosome expansion and establishment of normal sperm morphology during spermatogenesis | SPACA1 is recognized by anti-sperm antibodies in infertile males |
| PKC | Protein Kinase C | Predicted site of phosphorylation | Regulates numerous cellular responses including gene expression, protein secretion, cell proliferation, and the inflammatory response | |
| Cdk5 | Cyclin-dependent kinase 5 | Predicted site of phosphorylation | Plays a pivotal role in brain development (embryogenesis) and maintenance (adolescence and adulthood) | |
| Cdc2 | Cell Division Cycle 2 | Predicted site of phosphorylation | Regulates cell cycle progression | Also known as CDK1, or Cyclin Dependent Kinase 1 |

## Clinical significance and pathology
### Mutations - Single Nucleotide Polymorphisms (SNPs)

There exist many identified SNPs in the TMEM202 gene. Found in the table below include six of the most common to occur within the promoter region and coding sequence of TMEM202.

### SNPs in Human TMEM202

| SNP Name | SNP Location (Relative to TMEM202) | Mutation | Amino Acid Change | Frequency in human population (%) | Significance | Clinical Significance |
| rs74622826 | 164 bases upstream | G → A | Glycine → Glutamate | 0.25 | In promoter region | None reported in ClinVar |
| rs74343303 | 193 bases upstream | A→ C/G | Leucine → Leucine (Does not change) | 0.01 | In promoter region | None reported in ClinVar |
| rs114543781 | 284 bases upstream | C → T | Proline → Leucine | 0.42 | In promoter region | None reported in ClinVar |
| rs112986603 | Base 117 | C → T | 32A → 32V | 0.09 | In coding sequence | None reported in ClinVar |
| rs16956904 | Base 631 | A → T | 204M → 204L | 3.71 | In coding sequence within transmembrane region 4 | None reported in ClinVar |
| rs35916586 | Base 679 | G → A/T/C | 219S → 219T / 219S / 219P | 0.01 | In coding sequence | None reported in ClinVar |
A small subset of the SNPs may have functional influences on TMEM202 based on where they occur. The SNP, rs16956904 at base 631, is within the fourth transmembrane region. While this is an area of importance, both the normal and SNP variation result in a hydrophobic amino acid. This could explain why no clinical / phenotypic discrepancies have been observed. SNP rs114543781, 284 bases upstream is present where transcription factor HOXB13 is predicted to bind. This transcription factor is involved in the developmental regulatory system that provides cells with positional identities along the anterior-posterior axis. SNP rs74343303, 193 bases upstream also interferes with FOXD3 binding. FOXD3 has the ability to act as a transcriptional activator and repressor.

## Conceptual translation of TMEM202

Key found on page 2.