TMPRSS15

transmembrane serine protease 15, the group of Type II transmembrane serine proteases|Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 21:18269116-18485879

Previous symbols: [ "PRSS7" ]

Links

ENSG00000154646 ∙ NCBI:5651 ∙ OMIM:606635 ∙ HGNC:9490 ∙ Uniprot:P98073 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital enteropathy due to enteropeptidase deficiency (Strong), mode of inheritance: AR
• congenital enteropathy due to enteropeptidase deficiency (Strong), mode of inheritance: AR
• congenital enteropathy due to enteropeptidase deficiency (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Enterokinase deficiency	AR	Gastrointestinal	The condition tends to self-resolve, but early in life, pancreatic enzyme replacement or hydrolyzed formula can be beneficial	Gastrointestinal	4180366; 4322674; 1147667; 943355; 6347801; 11719902

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMPRSS15 gene.

• not provided (29 variants)
• Enterokinase deficiency (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMPRSS15 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			2	85	7	94
missense			155	11	15	181
nonsense	18		1			19
start loss						0
frameshift	12	4				16
inframe indel			4			4
splice donor/acceptor (+/-2bp)		11	1			12
splice region			7	21		28
non coding			1	62	12	75
Total	30	15	164	158	34

Highest pathogenic variant AF is 0.0000463

Variants in TMPRSS15

This is a list of pathogenic ClinVar variants found in the TMPRSS15 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-18269991-C-T			Uncertain significance (May 31, 2022)
21-18269995-C-T			Uncertain significance (May 08, 2022)
21-18269997-G-A		not specified	Uncertain significance (Feb 21, 2024)
21-18270004-T-C		not specified	Uncertain significance (Feb 25, 2023)
21-18270013-T-C			Uncertain significance (Aug 21, 2022)
21-18270014-G-C			Likely benign (Sep 05, 2023)
21-18270025-C-T		not specified	Uncertain significance (Jun 23, 2022)
21-18270026-G-A			Likely benign (Jul 12, 2023)
21-18270030-C-T			Uncertain significance (May 28, 2022)
21-18270031-G-A			Uncertain significance (Jul 26, 2022)
21-18270031-G-T			Uncertain significance (Jul 30, 2022)
21-18270042-G-A		not specified	Uncertain significance (Dec 07, 2021)
21-18270070-C-T			Uncertain significance (Jun 13, 2022)
21-18270076-G-C			Uncertain significance (May 24, 2022)
21-18270085-T-C			Uncertain significance (Aug 23, 2022)
21-18270101-C-G			Uncertain significance (Mar 27, 2022)
21-18270102-A-G		not specified	Uncertain significance (Oct 13, 2023)
21-18270117-G-A		not specified	Uncertain significance (Apr 23, 2024)
21-18270122-C-T			Likely benign (Dec 22, 2023)
21-18270123-C-T		not specified	Uncertain significance (Mar 20, 2024)
21-18270124-C-T			Likely benign (Jan 16, 2024)
21-18270144-A-G			Likely benign (May 05, 2022)
21-18275191-C-A			Uncertain significance (Jul 17, 2022)
21-18275206-A-T		not specified	Uncertain significance (Oct 06, 2023)
21-18275214-C-T		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMPRSS15	protein_coding	protein_coding	ENST00000284885	25	216765

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.58e-32	0.000224	125287	1	459	125747	0.00183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.860	582	526	1.11	0.0000264	6708
Missense in Polyphen		203	185.35	1.0952		2391
Synonymous	-0.676	204	192	1.06	0.0000106	1885
Loss of Function	0.613	51	56.0	0.911	0.00000280	687

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00334	0.00334
Ashkenazi Jewish	0.00	0.00
East Asian	0.000816	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.00238	0.00235
Middle Eastern	0.000816	0.000816
South Asian	0.00170	0.00154
Other	0.00459	0.00457

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Responsible for initiating activation of pancreatic proteolytic proenzymes (trypsin, chymotrypsin and carboxypeptidase A). It catalyzes the conversion of trypsinogen to trypsin which in turn activates other proenzymes including chymotrypsinogen, procarboxypeptidases, and proelastases.
• Disease: DISEASE: Enterokinase deficiency (ENTKD) [MIM:226200]: Life- threatening intestinal malabsorption disorder characterized by diarrhea and failure to thrive. {ECO:0000269|PubMed:11719902}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.245

Intolerance Scores

• rvis_EVS: 1.92
• rvis_percentile_EVS: 97.45

Haploinsufficiency Scores

• pHI: 0.0728
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmprss15
• Phenotype: immune system phenotype; growth/size/body region phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: proteolysis;receptor-mediated endocytosis
• Cellular component: brush border;membrane;integral component of membrane
• Molecular function: serine-type endopeptidase activity;scavenger receptor activity;protein binding