VSTM5

V-set and transmembrane domain containing 5, the group of V-set domain containing

Basic information

Region (hg38): 11:93818232-93850618

Previous symbols: [ "C11orf90" ]

Links

ENSG00000214376 ∙ NCBI:387804 ∙ ∙ HGNC:34443 ∙ Uniprot:A8MXK1 ∙ 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 VSTM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSTM5 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in VSTM5

This is a list of pathogenic ClinVar variants found in the VSTM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-93820785-A-G		not specified	Uncertain significance (Aug 30, 2021)
11-93820799-C-G		not specified	Uncertain significance (Dec 28, 2023)
11-93820807-G-T		not specified	Uncertain significance (Jan 26, 2023)
11-93821041-C-G		not specified	Uncertain significance (Oct 13, 2023)
11-93821041-C-T		not specified	Likely benign (Nov 17, 2022)
11-93821047-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-93821062-T-C		not specified	Uncertain significance (Jan 23, 2024)
11-93821108-C-T		not specified	Uncertain significance (Dec 19, 2023)
11-93821111-T-C		not specified	Uncertain significance (Jul 25, 2023)
11-93821125-A-G		not specified	Uncertain significance (Jul 14, 2021)
11-93821137-T-C		not specified	Uncertain significance (May 08, 2024)
11-93821144-G-T		not specified	Uncertain significance (Oct 22, 2021)
11-93821191-G-A		not specified	Uncertain significance (Aug 12, 2021)
11-93821210-A-T		not specified	Uncertain significance (May 24, 2023)
11-93821231-C-T		not specified	Uncertain significance (May 14, 2024)
11-93850468-C-T		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSTM5	protein_coding	protein_coding	ENST00000409977	4	32300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.25e-8	0.0765	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.979	83	112	0.740	0.00000621	1291
Missense in Polyphen		34	39.716	0.85608		440
Synonymous	0.194	47	48.7	0.965	0.00000305	406
Loss of Function	-0.595	10	8.17	1.22	3.50e-7	101

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

• Function: FUNCTION: Cell adhesion-like membrane protein of the central nervous system (CNS) which modulates both the position and complexity of central neurons by altering their membrane morphology and dynamics. Involved in the formation of neuronal dendrites and protrusions including dendritic filopodia. In synaptogenesis, regulates synapse formation by altering dendritic spine morphology and actin distribution. Promotes formation of unstable neuronal spines such as thin and branched types. Regulates neuronal morphogenesis and migration during cortical development in the brain. {ECO:0000250|UniProtKB:Q9D806}.

Intolerance Scores

• rvis_EVS: 1.3
• rvis_percentile_EVS: 93.94

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: Vstm5

Gene ontology

• Biological process: ventral spinal cord development;filopodium assembly;protein homooligomerization;positive regulation of excitatory synapse assembly
• Cellular component: plasma membrane;integral component of membrane;axon;dendrite