VSTM4

V-set and transmembrane domain containing 4, the group of V-set domain containing

Basic information

Region (hg38): 10:49014235-49115522

Previous symbols: [ "C10orf72" ]

Links

ENSG00000165633 ∙ NCBI:196740 ∙ ∙ HGNC:26470 ∙ Uniprot:Q8IW00 ∙ 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 VSTM4 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSTM4 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in VSTM4

This is a list of pathogenic ClinVar variants found in the VSTM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-49019659-G-C		not specified	Uncertain significance (May 03, 2023)
10-49019700-G-T		not specified	Uncertain significance (Dec 21, 2023)
10-49019718-G-A		not specified	Uncertain significance (Feb 06, 2024)
10-49019751-T-C		not specified	Uncertain significance (Feb 06, 2023)
10-49019757-T-A		not specified	Uncertain significance (Mar 13, 2023)
10-49046987-G-A		not specified	Uncertain significance (May 22, 2023)
10-49047041-G-A		not specified	Uncertain significance (Dec 16, 2023)
10-49048487-G-T		not specified	Uncertain significance (Jun 06, 2023)
10-49048493-C-T		not specified	Uncertain significance (Jan 08, 2024)
10-49048522-C-T		not specified	Uncertain significance (Oct 12, 2021)
10-49048537-G-A		not specified	Uncertain significance (Feb 17, 2022)
10-49077314-T-C		not specified	Uncertain significance (Nov 30, 2022)
10-49077318-C-T		not specified	Likely benign (Feb 27, 2023)
10-49107675-C-T		not specified	Uncertain significance (Oct 22, 2021)
10-49107684-C-G		not specified	Uncertain significance (Dec 07, 2021)
10-49107695-G-A		not specified	Uncertain significance (Jun 30, 2023)
10-49107735-G-A		not specified	Uncertain significance (Sep 16, 2021)
10-49107776-C-A		not specified	Uncertain significance (May 09, 2023)
10-49107797-T-A		not specified	Uncertain significance (Sep 06, 2022)
10-49107801-C-T		not specified	Uncertain significance (Jun 11, 2021)
10-49107909-C-T		not specified	Uncertain significance (Dec 13, 2023)
10-49107986-G-A		not specified	Uncertain significance (Jul 13, 2021)
10-49107993-C-A		not specified	Uncertain significance (Jan 03, 2024)
10-49115458-C-T		not specified	Uncertain significance (Aug 09, 2021)
10-49115463-G-A		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSTM4	protein_coding	protein_coding	ENST00000332853	8	101265

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0338	0.959	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.295	174	185	0.939	0.0000118	2043
Missense in Polyphen		54	67.727	0.79732		771
Synonymous	0.469	77	82.4	0.934	0.00000564	655
Loss of Function	2.34	5	14.7	0.341	6.20e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000332	0.000326
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000823	0.0000791
Middle Eastern	0.000223	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Peptide Lv enhances L-type voltage-gated calcium channel (L-VGCC) currents in retinal photoreceptors. {ECO:0000250|UniProtKB:T1NXB5}.

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.16

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.488
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vstm4

Gene ontology

• Cellular component: extracellular region;plasma membrane;integral component of membrane