VSTM1

V-set and transmembrane domain containing 1, the group of Immunoglobulin like domain containing

Basic information

Region (hg38): 19:54040824-54063953

Links

ENSG00000189068 ∙ NCBI:284415 ∙ OMIM:616804 ∙ HGNC:29455 ∙ Uniprot:Q6UX27 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VSTM1 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSTM1 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in VSTM1

This is a list of pathogenic ClinVar variants found in the VSTM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54040965-A-T		not specified	Uncertain significance (Aug 22, 2023)
19-54040977-G-A		not specified	Uncertain significance (Jan 17, 2023)
19-54040978-C-T		not specified	Uncertain significance (Jan 04, 2024)
19-54041035-C-T		not specified	Uncertain significance (Nov 09, 2023)
19-54041038-T-C		not specified	Uncertain significance (Jun 29, 2023)
19-54041079-G-A		not specified	Uncertain significance (Oct 17, 2023)
19-54041814-C-T		not specified	Uncertain significance (Jul 28, 2021)
19-54042298-T-C		not specified	Uncertain significance (Feb 12, 2024)
19-54051441-G-C		not specified	Uncertain significance (Sep 14, 2022)
19-54058336-T-C		not specified	Uncertain significance (Mar 08, 2024)
19-54058429-C-T		not specified	Uncertain significance (Mar 29, 2022)
19-54058450-C-T		not specified	Uncertain significance (Apr 25, 2022)
19-54058452-T-C		not specified	Uncertain significance (Feb 28, 2024)
19-54058468-C-A		not specified	Uncertain significance (Apr 12, 2022)
19-54058486-C-T		not specified	Likely benign (Jul 17, 2023)
19-54058522-G-C		not specified	Uncertain significance (Jan 31, 2022)
19-54058535-C-G		not specified	Uncertain significance (Jul 05, 2023)
19-54058564-C-A		not specified	Uncertain significance (Jun 22, 2023)
19-54063758-G-A		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSTM1	protein_coding	protein_coding	ENST00000338372	9	23129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.37e-8	0.262	125683	0	63	125746	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.148	136	131	1.04	0.00000720	1531
Missense in Polyphen		36	30.362	1.1857		405
Synonymous	0.253	52	54.4	0.956	0.00000349	441
Loss of Function	0.436	12	13.7	0.873	5.82e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000242
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00239	0.00239
Finnish	0.000139	0.0000924
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00239	0.00239
South Asian	0.0000980	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 2: Behaves as a cytokine, promoting IL17A secretion by CD4+ T-cells, and differentiation and activation of IL17 producing helper T-cells (TH17).

Intolerance Scores

• loftool: 0.766
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.0455
• hipred: N
• hipred_score: 0.123
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00230

Gene Damage Prediction

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

Gene ontology

• Biological process: immune system process;regulation of signaling receptor activity
• Cellular component: extracellular space;integral component of membrane
• Molecular function: cytokine activity