VSIG1

V-set and immunoglobulin domain containing 1, the group of V-set domain containing|IgCAM CXADR-related subfamily

Basic information

Region (hg38): X:108044970-108079184

Links

ENSG00000101842 ∙ NCBI:340547 ∙ OMIM:300620 ∙ HGNC:28675 ∙ Uniprot:Q86XK7 ∙ 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 VSIG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSIG1 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				3	1	4
missense			6	3		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	8	7	1

Variants in VSIG1

This is a list of pathogenic ClinVar variants found in the VSIG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-108061477-A-G			Likely benign (Nov 30, 2018)
X-108061497-G-A		not specified	Uncertain significance (Jul 19, 2023)
X-108061509-C-T		not specified	Uncertain significance (Apr 25, 2023)
X-108067004-C-T			Benign (Apr 03, 2018)
X-108067036-A-T		not specified	Uncertain significance (Aug 12, 2021)
X-108072702-C-T			Likely benign (Oct 01, 2022)
X-108072742-T-C		not specified	Uncertain significance (Jan 24, 2024)
X-108072755-C-T		not specified	Likely benign (Mar 24, 2023)
X-108072811-G-A		not specified	Uncertain significance (Sep 27, 2021)
X-108073260-C-T			Likely benign (Mar 01, 2022)
X-108073347-C-T			Likely benign (Nov 01, 2022)
X-108076209-C-T		not specified	Uncertain significance (May 30, 2022)
X-108077066-C-A		not specified	Uncertain significance (Apr 18, 2023)
X-108077170-C-T			Likely benign (Nov 01, 2022)
X-108077238-G-T		not specified	Uncertain significance (May 17, 2023)
X-108077278-C-A			Likely benign (Apr 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSIG1	protein_coding	protein_coding	ENST00000415430	8	34215

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00239	0.933	125712	5	2	125719	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.456	152	169	0.901	0.0000130	2763
Missense in Polyphen		42	51.503	0.81549		877
Synonymous	-0.439	75	70.3	1.07	0.00000645	846
Loss of Function	1.62	6	12.1	0.498	9.77e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000741	0.0000741
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000725	0.0000544
Finnish	0.0000628	0.0000462
European (Non-Finnish)	0.0000122	0.00000879
Middle Eastern	0.0000725	0.0000544
South Asian	0.00	0.00
Other	0.000450	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0750

Intolerance Scores

• loftool: 0.482
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.374
• hipred: N
• hipred_score: 0.123
• ghis: 0.398

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: Vsig1
• Phenotype: digestive/alimentary phenotype

Gene ontology

• Biological process: epithelial cell morphogenesis;maintenance of gastrointestinal epithelium
• Cellular component: plasma membrane;integral component of membrane;basolateral plasma membrane