TMPRSS9

transmembrane serine protease 9, the group of Type II transmembrane serine proteases

Basic information

Region (hg38): 19:2360238-2426261

Links

ENSG00000178297 ∙ NCBI:360200 ∙ OMIM:610477 ∙ HGNC:30079 ∙ Uniprot:Q7Z410 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMPRSS9 gene.

• not_specified (240 variants)
• not_provided (15 variants)
• Global_developmental_delay (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMPRSS9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001395513.1. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	2	7
missense			216	26	3	245
nonsense		1				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	216	31	5

Highest pathogenic variant AF is 0.0000049563223

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMPRSS9	protein_coding	protein_coding	ENST00000332578	17	36469

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.62e-17	0.481	125321	2	425	125748	0.00170

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.22	744	656	1.13	0.0000431	6647
Missense in Polyphen		285	256.14	1.1127		2596
Synonymous	-1.79	336	297	1.13	0.0000213	2279
Loss of Function	1.73	33	45.6	0.723	0.00000247	479

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00197	0.00193
Ashkenazi Jewish	0.000313	0.000298
East Asian	0.00104	0.00103
Finnish	0.000711	0.000647
European (Non-Finnish)	0.00263	0.00245
Middle Eastern	0.00104	0.00103
South Asian	0.00196	0.00190
Other	0.00103	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serase-1 and serase-2 are serine proteases that hydrolyze the peptides N-t-Boc-Gln-Ala-Arg-AMC and N-t-Boc-Gln- Gly-Arg-AMC. In contrast, N-t-Boc-Ala-Phe-Lys-AMC and N-t-Boc-Ala- Pro-Ala-AMC are not significantly hydrolyzed.

Intolerance Scores

• loftool: 0.0742
• rvis_EVS: 1.65
• rvis_percentile_EVS: 96.19

Haploinsufficiency Scores

• pHI: 0.0712
• hipred: N
• hipred_score: 0.219

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.188

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmprss9

Gene ontology

• Biological process: proteolysis
• Cellular component: integral component of plasma membrane
• Molecular function: serine-type endopeptidase activity