TMPRSS5

transmembrane serine protease 5, the group of Scavenger receptor cysteine rich domain containing|Type II transmembrane serine proteases

Basic information

Region (hg38): 11:113687546-113706373

Links

ENSG00000166682 ∙ NCBI:80975 ∙ OMIM:606751 ∙ HGNC:14908 ∙ Uniprot:Q9H3S3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nonsyndromic genetic hearing loss (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMPRSS5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMPRSS5 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				4	8	12
missense			19	9	2	30
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			1	9	34	44
Total	0	0	20	22	45

Variants in TMPRSS5

This is a list of pathogenic ClinVar variants found in the TMPRSS5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-113688123-G-A			Benign (May 19, 2021)
11-113688168-G-A			Likely benign (Jul 05, 2018)
11-113688329-G-A			Likely benign (Jul 23, 2018)
11-113689755-C-T		not specified	Benign (Dec 31, 2019)
11-113689859-A-C		not specified	Uncertain significance (Dec 02, 2021)
11-113689864-C-T		TMPRSS5-related disorder	Likely benign (May 23, 2019)
11-113689871-C-T		not specified	Likely benign (Oct 25, 2023)
11-113690184-A-C			Benign (May 19, 2021)
11-113690190-A-C			Benign (Jun 16, 2018)
11-113690196-A-C			Benign (Jun 13, 2018)
11-113690247-C-T		not specified	Conflicting classifications of pathogenicity (Jun 11, 2021)
11-113690266-C-A			Likely benign (Jul 09, 2018)
11-113690278-G-A			Likely benign (Dec 12, 2018)
11-113690279-G-A		not specified	Benign/Likely benign (Apr 26, 2018)
11-113690294-G-A			Benign (Dec 31, 2019)
11-113690303-G-A		not specified	Benign (Sep 13, 2017)
11-113690325-G-C		not specified	Uncertain significance (Feb 28, 2024)
11-113690332-A-G		not specified	Benign (May 09, 2017)
11-113690335-A-G		not specified	Benign (May 09, 2017)
11-113690345-C-G		TMPRSS5-related disorder	Likely benign (Jun 19, 2019)
11-113690357-C-T		not specified	Uncertain significance (Feb 16, 2023)
11-113690525-T-C			Benign (May 15, 2021)
11-113690534-G-A			Benign (May 15, 2021)
11-113690699-A-C			Benign (Nov 12, 2018)
11-113690759-AG-A			Benign (Jun 24, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMPRSS5	protein_coding	protein_coding	ENST00000299882	13	18824

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.26e-9	0.685	124554	0	86	124640	0.000345

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.923	212	253	0.837	0.0000151	2855
Missense in Polyphen		58	71.926	0.80639		801
Synonymous	0.619	94	102	0.922	0.00000642	899
Loss of Function	1.37	17	24.3	0.700	0.00000113	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000783	0.000740
Ashkenazi Jewish	0.00	0.00
East Asian	0.000413	0.000389
Finnish	0.000279	0.000278
European (Non-Finnish)	0.000461	0.000442
Middle Eastern	0.000413	0.000389
South Asian	0.0000757	0.0000654
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in hearing. {ECO:0000269|PubMed:17918732}.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.04

Haploinsufficiency Scores

• pHI: 0.0987
• hipred: N
• hipred_score: 0.167
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmprss5

Gene ontology

• Biological process: proteolysis;receptor-mediated endocytosis
• Cellular component: plasma membrane;integral component of membrane;neuronal cell body
• Molecular function: serine-type endopeptidase activity;scavenger receptor activity;peptidase activity