TMPRSS13
protein-codingtransmembrane serine protease 13, the group of Type II transmembrane serine proteases|Scavenger receptor cysteine rich domain containing
Gene summary
This gene encodes a member of the type II transmembrane serine protease family. The encoded protein contains a type II transmembrane domain, a receptor class A domain, a scavenger receptor cysteine-rich domain and a protease domain. Transmembrane serine proteases are regulated by protease inhibitors and known to function in development, homeostasis, infection, and tumorigenesis. This protein facilitates entry of viruses into host cells by proteolytically cleaving and activating viral envelope glycoproteins. [provided by RefSeq, Aug 2021]
- TMPRSS11
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TMPRSS13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001077263.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 82 | 2 | 84 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 82 | 3 | 0 | 85 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001070731.1 | 13 | MANE Select | |
| Ensembl | ENSP00000434279.1 | 13 | MANE Select | |
| RefSeq | NP_001193718.1 | 12 | Standard | |
| RefSeq | NP_001193719.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Influenza A - Homo sapiens (human)
Biological Process
- proteolysis
- receptor-mediated endocytosis
Molecular Function
- serine-type endopeptidase activity
- scavenger receptor activity
Cellular Component
- integral component of membrane
- blood microparticle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000524993
- Coding exons
- 13
- Length
- 28817
- Individuals with no LoFs
- 123414
- Homozygous LoFs
- 29
- Heterozygous LoFs
- 1476
- Defined
- 124919
- p
- 0.00604
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 288 | 341 | 0.846 | 0.0000201 | 3628 |
| Missense (PolyPhen) | 78 | 107.61 | 0.72482 | 1228 | ||
| Synonymous | 0.551 | 129 | 137 | 0.940 | 0.00000863 | 1174 |
| Loss of Function | 1.99 | 17 | 28.4 | 0.598 | 0.00000139 | 311 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00060 | 0.00045 | rare |
| Latino/Admixed American | 0.065 | 0.032 | notable |
| Ashkenazi Jewish | 0.0046 | 0.0023 | notable |
| East Asian | 0.0019 | 0.0011 | notable |
| Finnish | 0.00038 | 0.00023 | rare |
| European (Non-Finnish) | 0.0027 | 0.0014 | notable |
| South Asian | 0.011 | 0.0057 | notable |
| Other | 0.011 | 0.0054 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.180
Intolerance Scores
- LoFtool
- 0.344
- RVIS EVS
- 0.67
- RVIS percentile EVS
- 84.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.802
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |