VSIG2

V-set and immunoglobulin domain containing 2, the group of V-set domain containing|IgCAM CXADR-related subfamily|I-set domain containing

Basic information

Region (hg38): 11:124747474-124752255

Links

ENSG00000019102 ∙ NCBI:23584 ∙ OMIM:606011 ∙ HGNC:17149 ∙ Uniprot:Q96IQ7 ∙ 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 VSIG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSIG2 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	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	0

Variants in VSIG2

This is a list of pathogenic ClinVar variants found in the VSIG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-124747591-G-T		not specified	Uncertain significance (Dec 13, 2022)
11-124747596-T-C		not specified	Uncertain significance (May 24, 2023)
11-124747606-C-T		not specified	Uncertain significance (Oct 03, 2024)
11-124747627-T-C		not specified	Likely benign (Dec 16, 2022)
11-124748400-T-C		not specified	Uncertain significance (Jul 26, 2024)
11-124748411-G-A		not specified	Uncertain significance (Nov 18, 2022)
11-124748432-C-T		not specified	Uncertain significance (Sep 26, 2024)
11-124748462-G-A		not specified	Likely benign (Oct 26, 2022)
11-124748519-C-T		not specified	Uncertain significance (Oct 16, 2023)
11-124748670-G-T		not specified	Uncertain significance (Aug 04, 2023)
11-124748703-C-T		not specified	Uncertain significance (Aug 29, 2024)
11-124748704-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-124748710-T-C		not specified	Uncertain significance (Dec 07, 2023)
11-124748719-A-T		not specified	Uncertain significance (Sep 26, 2024)
11-124748732-G-C		not specified	Uncertain significance (Apr 13, 2022)
11-124748742-A-G		not specified	Uncertain significance (Nov 23, 2022)
11-124749715-C-G		not specified	Uncertain significance (Sep 29, 2022)
11-124749752-C-T		not specified	Likely benign (Jul 25, 2023)
11-124749753-G-A		not specified	Uncertain significance (Oct 12, 2022)
11-124749782-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-124749813-A-G		not specified	Uncertain significance (Dec 05, 2024)
11-124749863-G-C		not specified	Uncertain significance (Sep 09, 2021)
11-124750728-T-G		not specified	Uncertain significance (Feb 28, 2024)
11-124750762-G-T		not specified	Uncertain significance (Nov 22, 2022)
11-124750839-A-T		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSIG2	protein_coding	protein_coding	ENST00000326621	7	4767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000120	0.848	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.648	210	185	1.13	0.00000980	2062
Missense in Polyphen		64	64.341	0.99471		727
Synonymous	0.549	76	82.3	0.923	0.00000461	723
Loss of Function	1.31	8	13.1	0.609	6.08e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000873	0.000872
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0917

Intolerance Scores

• loftool: 0.673
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.162
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.386

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vsig2

Gene ontology

• Cellular component: integral component of plasma membrane;membrane