VSTM2L

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

Basic information

Region (hg38): 20:37903111-37945350

Previous symbols: [ "C20orf102" ]

Links

ENSG00000132821 ∙ NCBI:128434 ∙ OMIM:616537 ∙ HGNC:16096 ∙ Uniprot:Q96N03 ∙ 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 VSTM2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSTM2L 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in VSTM2L

This is a list of pathogenic ClinVar variants found in the VSTM2L region.

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

Position	Type	Phenotype	Significance	ClinVar
20-37903358-C-T		not specified	Uncertain significance (Feb 06, 2023)
20-37903370-T-C		not specified	Uncertain significance (Feb 27, 2023)
20-37903420-G-T		not specified	Uncertain significance (Mar 19, 2024)
20-37903432-G-A		not specified	Uncertain significance (Feb 05, 2024)
20-37903448-G-T		not specified	Uncertain significance (Apr 06, 2024)
20-37931670-C-T		not specified	Uncertain significance (Aug 30, 2021)
20-37931671-G-A		not specified	Uncertain significance (May 14, 2024)
20-37931754-G-A		not specified	Uncertain significance (Jun 07, 2023)
20-37931758-G-A		not specified	Uncertain significance (Sep 27, 2022)
20-37931778-G-C		not specified	Uncertain significance (Oct 27, 2023)
20-37933563-G-T		not specified	Uncertain significance (Jan 23, 2023)
20-37943993-G-A		not specified	Uncertain significance (Jan 26, 2022)
20-37944027-C-T		not specified	Uncertain significance (Jan 06, 2023)
20-37944042-C-T		not specified	Uncertain significance (May 23, 2023)
20-37944059-G-A		not specified	Uncertain significance (Oct 12, 2022)
20-37944065-C-T		not specified	Uncertain significance (Mar 26, 2024)
20-37944073-C-G		not specified	Uncertain significance (May 30, 2023)
20-37944114-C-T		not specified	Uncertain significance (Dec 12, 2023)
20-37944140-A-G		not specified	Uncertain significance (Nov 07, 2022)
20-37944173-G-A		not specified	Uncertain significance (May 26, 2023)
20-37944173-G-C		not specified	Uncertain significance (Jun 18, 2021)
20-37944178-G-A			Likely benign (Nov 01, 2022)
20-37944221-C-T		not specified	Uncertain significance (Dec 12, 2023)
20-37944222-G-A		not specified	Uncertain significance (Jan 18, 2023)
20-37944243-G-A		not specified	Uncertain significance (May 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSTM2L	protein_coding	protein_coding	ENST00000373461	4	42254

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.247	0.727	125703	0	6	125709	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.200	115	121	0.949	0.00000859	1288
Missense in Polyphen		41	50.736	0.8081		466
Synonymous	-0.720	64	57.1	1.12	0.00000457	422
Loss of Function	1.86	2	7.48	0.267	3.20e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Haploinsufficiency Scores

• pHI: 0.587
• hipred: N
• hipred_score: 0.371
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.317

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vstm2l

Gene ontology

• Biological process: homophilic cell adhesion via plasma membrane adhesion molecules;axon guidance;negative regulation of neuron apoptotic process;dendrite self-avoidance
• Cellular component: extracellular region;cytoplasm;plasma membrane;axon
• Molecular function: protein binding;cell-cell adhesion mediator activity