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 (Supportive), mode of inheritance: AR
congenital enteropathy due to enteropeptidase deficiency (Strong), mode of inheritance: AR
congenital enteropathy due to enteropeptidase deficiency (Strong), 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 (471 variants)
not_specified (138 variants)
Enterokinase_deficiency (26 variants)
TMPRSS15-related_disorder (15 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. These statistics are base on transcript: NM_000002772.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	122 clinvar	5 clinvar	129
missense		2 clinvar	221 clinvar	22 clinvar	12 clinvar	257
nonsense	24 clinvar	2 clinvar	2 clinvar			28
start loss						0
frameshift	18 clinvar	9 clinvar				27
splice donor/acceptor (+/-2bp)		18 clinvar	1 clinvar			19
Total	42	31	226	144	17

Highest pathogenic variant AF is 0.00133151

Loading clinvar variants...

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

loftool
rvis_EVS: 1.92
rvis_percentile_EVS: 97.45

Haploinsufficiency Scores

pHI: 0.0728
hipred: N
hipred_score: 0.146
ghis

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