TMPRSS13

transmembrane serine protease 13, the group of Type II transmembrane serine proteases|Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 11:117900641-117929459

Previous symbols: [ "TMPRSS11" ]

Links

ENSG00000137747 ∙ NCBI:84000 ∙ OMIM:610050 ∙ HGNC:29808 ∙ Uniprot:Q9BYE2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMPRSS13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMPRSS13 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	0

Variants in TMPRSS13

This is a list of pathogenic ClinVar variants found in the TMPRSS13 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-117903684-C-A		not specified	Uncertain significance (Oct 26, 2022)
11-117903767-C-T		not specified	Uncertain significance (May 03, 2023)
11-117903981-C-T		not specified	Uncertain significance (May 23, 2024)
11-117904080-C-T			Uncertain significance (Jun 28, 2020)
11-117905648-C-A		not specified	Uncertain significance (Apr 08, 2024)
11-117905728-G-A		not specified	Uncertain significance (May 16, 2023)
11-117908620-G-T			Uncertain significance (Jun 28, 2020)
11-117908639-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-117908641-A-G		not specified	Uncertain significance (Dec 07, 2021)
11-117908699-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-117908738-T-C		not specified	Uncertain significance (Jun 18, 2021)
11-117908747-C-T		not specified	Uncertain significance (Oct 13, 2023)
11-117908780-G-A		not specified	Uncertain significance (Aug 17, 2022)
11-117909890-C-G		not specified	Uncertain significance (Nov 09, 2021)
11-117909941-C-T		not specified	Uncertain significance (Nov 28, 2023)
11-117910731-G-A		not specified	Uncertain significance (May 08, 2023)
11-117913874-T-A		not specified	Uncertain significance (May 05, 2022)
11-117913874-T-C		not specified	Likely benign (Sep 29, 2023)
11-117914449-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-117914457-G-A		not specified	Uncertain significance (Jan 05, 2022)
11-117914462-G-C		not specified	Uncertain significance (May 17, 2023)
11-117914484-C-G		not specified	Uncertain significance (Aug 31, 2022)
11-117914509-A-G		not specified	Uncertain significance (Dec 27, 2023)
11-117917203-G-T		not specified	Uncertain significance (Oct 12, 2022)
11-117917206-G-T		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMPRSS13	protein_coding	protein_coding	ENST00000524993	13	28817

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-8	0.953	123414	29	1476	124919	0.00604

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	288	341	0.846	0.0000201	3628
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0654	0.0652
Ashkenazi Jewish	0.00460	0.00229
East Asian	0.00191	0.00106
Finnish	0.000376	0.000232
European (Non-Finnish)	0.00267	0.00143
Middle Eastern	0.00191	0.00106
South Asian	0.0112	0.00573
Other	0.0112	0.00544

dbNSFP

Source: dbNSFP

• Pathway: Influenza A - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.180

Intolerance Scores

• loftool: 0.344
• rvis_EVS: 0.67
• rvis_percentile_EVS: 84.64

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.199
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.802

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tmprss13
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); normal phenotype

Gene ontology

• Biological process: proteolysis;receptor-mediated endocytosis
• Cellular component: integral component of membrane;blood microparticle
• Molecular function: serine-type endopeptidase activity;scavenger receptor activity