VSTM2B

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

Basic information

Region (hg38): 19:29525994-29564551

Links

ENSG00000187135 ∙ NCBI:342865 ∙ ∙ HGNC:33595 ∙ Uniprot:A6NLU5 ∙ 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 VSTM2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSTM2B 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					1	1
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	1

Variants in VSTM2B

This is a list of pathogenic ClinVar variants found in the VSTM2B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-29526624-C-T		not specified	Uncertain significance (Oct 25, 2022)
19-29526638-C-T		not specified	Uncertain significance (Aug 28, 2023)
19-29526648-T-A		not specified	Uncertain significance (Dec 20, 2023)
19-29526662-G-A		not specified	Uncertain significance (Mar 16, 2022)
19-29527234-G-A		not specified	Uncertain significance (May 20, 2024)
19-29527270-C-T		not specified	Uncertain significance (Sep 07, 2022)
19-29527291-G-A		not specified	Uncertain significance (Sep 29, 2023)
19-29527324-T-G		not specified	Uncertain significance (Dec 28, 2022)
19-29527342-C-T		not specified	Uncertain significance (Aug 04, 2023)
19-29527373-G-A		not specified	Uncertain significance (Feb 27, 2023)
19-29527384-G-T		not specified	Uncertain significance (Dec 26, 2023)
19-29529855-C-T		not specified	Uncertain significance (Mar 29, 2022)
19-29529886-A-T		not specified	Uncertain significance (Aug 01, 2022)
19-29529912-G-C		not specified	Uncertain significance (Jan 23, 2024)
19-29529954-A-C		not specified	Likely benign (Apr 07, 2023)
19-29529967-T-C		not specified	Uncertain significance (Jun 22, 2022)
19-29530002-G-A		not specified	Uncertain significance (Jan 27, 2022)
19-29530044-G-C		not specified	Uncertain significance (Nov 10, 2022)
19-29530051-C-A		not specified	Uncertain significance (Feb 15, 2023)
19-29530056-G-T		not specified	Uncertain significance (Jul 20, 2021)
19-29530103-G-T		not specified	Uncertain significance (Dec 27, 2023)
19-29530113-G-A		not specified	Uncertain significance (May 26, 2024)
19-29530113-G-T		not specified	Uncertain significance (Apr 25, 2023)
19-29530123-G-C		not specified	Uncertain significance (Nov 10, 2022)
19-29530138-G-T		not specified	Uncertain significance (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSTM2B	protein_coding	protein_coding	ENST00000335523	5	37981

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00316	0.835	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.136	138	134	1.03	0.00000674	1765
Missense in Polyphen		37	40.054	0.92376		472
Synonymous	0.257	58	60.5	0.958	0.00000308	637
Loss of Function	1.16	5	8.69	0.575	3.81e-7	108

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.197
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.414

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vstm2b

Gene ontology

• Cellular component: integral component of membrane