TMPRSS4

transmembrane serine protease 4, the group of Type II transmembrane serine proteases|Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 11:118077011-118121890

Links

ENSG00000137648 ∙ NCBI:56649 ∙ OMIM:606565 ∙ HGNC:11878 ∙ Uniprot:Q9NRS4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive cerebral atrophy (Supportive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMPRSS4 gene.

• Inborn genetic diseases (17 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMPRSS4 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			15	4		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	15	5	0

Variants in TMPRSS4

This is a list of pathogenic ClinVar variants found in the TMPRSS4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118094822-G-A		not specified	Uncertain significance (Jan 30, 2024)
11-118098999-C-T		not specified	Uncertain significance (Jan 23, 2023)
11-118099072-C-T			Likely benign (Nov 21, 2019)
11-118103191-G-C		not specified	Uncertain significance (Dec 18, 2023)
11-118103213-G-C		not specified	Uncertain significance (Aug 02, 2021)
11-118103216-C-G		not specified	Uncertain significance (Jan 24, 2024)
11-118103229-T-C		not specified	Uncertain significance (Jun 03, 2022)
11-118104694-G-A		not specified	Uncertain significance (Jun 02, 2023)
11-118104709-G-A		not specified	Uncertain significance (Dec 04, 2023)
11-118104754-C-A		not specified	Uncertain significance (Feb 10, 2022)
11-118107857-G-A		not specified	Likely benign (Jan 03, 2024)
11-118108857-C-G		not specified	Uncertain significance (Jun 26, 2023)
11-118108891-G-C			Likely benign (Nov 01, 2022)
11-118111842-G-A		not specified	Likely benign (Jun 02, 2023)
11-118113273-C-T		not specified	Uncertain significance (Sep 06, 2022)
11-118113322-G-T		not specified	Uncertain significance (Sep 01, 2021)
11-118113357-A-G		not specified	Likely benign (May 18, 2022)
11-118115136-A-G			Likely benign (Oct 10, 2018)
11-118115210-C-T		not specified	Uncertain significance (Jun 05, 2023)
11-118115223-A-T		not specified	Uncertain significance (Mar 07, 2023)
11-118115246-C-T		not specified	Uncertain significance (Dec 17, 2023)
11-118115267-T-G		not specified	Uncertain significance (Jan 03, 2022)
11-118115270-A-T		not specified	Uncertain significance (Nov 12, 2021)
11-118117314-G-C		not specified	Uncertain significance (Dec 20, 2021)
11-118117314-G-T		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMPRSS4	protein_coding	protein_coding	ENST00000437212	13	44853

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.21e-8	0.797	125666	0	81	125747	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.347	242	258	0.939	0.0000142	2866
Missense in Polyphen		75	79.205	0.94692		882
Synonymous	0.335	98	102	0.958	0.00000627	829
Loss of Function	1.51	16	24.0	0.668	0.00000111	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00247	0.00234
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000244	0.000237
Middle Eastern	0.000163	0.000163
South Asian	0.000346	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable protease. Seems to be capable of activating ENaC (By similarity). {ECO:0000250}.
• Pathway: Influenza A - Homo sapiens (human);EMT transition in Colorectal Cancer (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.139
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.98

Haploinsufficiency Scores

• pHI: 0.274
• hipred: N
• hipred_score: 0.208
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.214

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmprss4
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: tmprss4a
• Affected structure: keratinocyte
• Phenotype tag: abnormal
• Phenotype quality: detached from

Gene ontology

• Biological process: proteolysis;receptor-mediated endocytosis;response to wounding;regulation of gene expression;negative regulation of growth rate
• Cellular component: integral component of membrane;secretory granule
• Molecular function: serine-type endopeptidase activity;scavenger receptor activity;protein binding