VSIG10

V-set and immunoglobulin domain containing 10, the group of V-set domain containing|I-set domain containing

Basic information

Region (hg38): 12:118063592-118136026

Links

ENSG00000176834 ∙ NCBI:54621 ∙ ∙ HGNC:26078 ∙ Uniprot:Q8N0Z9 ∙ 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 VSIG10 gene.

• Inborn genetic diseases (25 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSIG10 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	1

Variants in VSIG10

This is a list of pathogenic ClinVar variants found in the VSIG10 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-118066652-T-C		not specified	Uncertain significance (May 23, 2023)
12-118066668-T-C		not specified	Uncertain significance (Mar 30, 2022)
12-118068407-G-C		not specified	Uncertain significance (Dec 15, 2022)
12-118068440-T-C		not specified	Uncertain significance (Dec 12, 2023)
12-118068451-T-C		not specified	Likely benign (Jun 27, 2023)
12-118068473-G-T		not specified	Uncertain significance (Nov 14, 2023)
12-118068514-G-A		not specified	Uncertain significance (Jan 12, 2024)
12-118068522-TTCCTCC-T		not specified	Benign (Mar 29, 2016)
12-118071382-T-C		not specified	Uncertain significance (Jan 23, 2023)
12-118073704-A-T		not specified	Uncertain significance (Sep 20, 2023)
12-118073774-C-T		not specified	Uncertain significance (Aug 08, 2023)
12-118073818-C-A		not specified	Uncertain significance (Mar 01, 2024)
12-118073864-C-T		not specified	Uncertain significance (Dec 21, 2022)
12-118073866-G-C		not specified	Uncertain significance (Sep 15, 2021)
12-118073935-G-A		not specified	Uncertain significance (Aug 13, 2021)
12-118073962-T-C		not specified	Uncertain significance (Sep 14, 2023)
12-118079419-A-T		not specified	Uncertain significance (Nov 07, 2022)
12-118079477-A-G		not specified	Uncertain significance (Mar 28, 2023)
12-118079505-A-G		not specified	Uncertain significance (Jul 31, 2023)
12-118079534-C-T		not specified	Uncertain significance (Apr 19, 2023)
12-118079545-C-G		not specified	Uncertain significance (Mar 06, 2023)
12-118079546-T-G		not specified	Uncertain significance (Mar 06, 2023)
12-118082352-A-T		not specified	Uncertain significance (Dec 27, 2023)
12-118082364-C-T		not specified	Uncertain significance (Dec 01, 2022)
12-118082378-T-C		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSIG10	protein_coding	protein_coding	ENST00000359236	9	72434

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000348	0.988	124575	1	79	124655	0.000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.583	266	294	0.904	0.0000155	3497
Missense in Polyphen		54	71.513	0.75511		858
Synonymous	-0.372	128	123	1.04	0.00000720	1074
Loss of Function	2.27	13	25.3	0.514	0.00000124	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000445	0.000439
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000153	0.000150
Middle Eastern	0.000111	0.000111
South Asian	0.00160	0.00157
Other	0.000501	0.000495

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.23

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.469

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	High	Medium	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Vsig10

Gene ontology

• Cellular component: integral component of membrane