VSTM2A

V-set and transmembrane domain containing 2A, the group of V-set domain containing

Basic information

Region (hg38): 7:54542325-54571080

Previous symbols: [ "VSTM2" ]

Links

ENSG00000170419 ∙ NCBI:222008 ∙ ∙ HGNC:28499 ∙ Uniprot:Q8TAG5 ∙ 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 VSTM2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSTM2A 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in VSTM2A

This is a list of pathogenic ClinVar variants found in the VSTM2A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-54542774-C-A		not specified	Uncertain significance (Feb 26, 2024)
7-54542776-G-T		not specified	Uncertain significance (Aug 10, 2021)
7-54544695-G-C		not specified	Uncertain significance (Jul 16, 2021)
7-54544744-G-A		not specified	Uncertain significance (Jan 06, 2023)
7-54544750-G-A		not specified	Uncertain significance (Feb 27, 2024)
7-54544757-T-C		not specified	Uncertain significance (Dec 14, 2021)
7-54546968-G-A		not specified	Uncertain significance (Jan 17, 2024)
7-54546971-C-G		not specified	Uncertain significance (Mar 20, 2024)
7-54549843-G-A		not specified	Uncertain significance (May 02, 2024)
7-54549853-A-T		not specified	Uncertain significance (Jun 28, 2022)
7-54549889-G-A		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSTM2A	protein_coding	protein_coding	ENST00000407838	5	28756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.273	0.723	125500	0	4	125504	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.625	114	134	0.848	0.00000662	1530
Missense in Polyphen		38	54.433	0.69811		640
Synonymous	-0.663	63	56.7	1.11	0.00000315	454
Loss of Function	2.44	3	12.2	0.246	6.28e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000496	0.0000462
European (Non-Finnish)	0.0000292	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of the early stage of white and brown preadipocyte cell differentiation. Promotes adipogenic commitment of preadipocytes by increasing gene expression of the transcription factor PPARG in a BMP4-dependent signaling pathway. {ECO:0000269|PubMed:28052263}.

Intolerance Scores

• loftool: 0.714
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.174
• hipred: N
• hipred_score: 0.439
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0165

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vstm2a

Gene ontology

• Biological process: positive regulation of gene expression;positive regulation of lipid storage;cell differentiation;positive regulation of white fat cell proliferation;cellular response to BMP stimulus;positive regulation of brown fat cell differentiation
• Cellular component: extracellular region;nucleus;integral component of membrane
• Molecular function: identical protein binding