VSIG1

protein-coding

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

Gene summary

This gene encodes a member of the junctional adhesion molecule (JAM) family. The encoded protein contains multiple glycosylation sites at the N-terminal region, and multiple phosphorylation sites and glutamic acid/proline (EP) repeats at the C-terminal region. The gene is expressed in normal stomach and testis, as well as in gastric, esophageal and ovarian cancers. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]

MANE transcript

NM_182607.5

Inheritance

—

ClinVar variants

U:50B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chrX:108,044,970-108,079,184

External References & Databases

Ensembl (ENSG00000101842)

Transcript & Mutation Effects

hg38 • Region Span ~34.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VSIG1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 33

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182607.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			7 clinvar	3 clinvar	1 clinvar	11
missense			38 clinvar	7 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	50	10	1	61

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182607.5	RefSeq	NP_872413.1	7	MANE Select
ENST00000217957.10	Ensembl	ENSP00000217957.3	7	MANE Select
NM_001170553.2	RefSeq	NP_001164024.1	8	Standard
ENST00000415430.7	Ensembl	ENSP00000402219.3	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

epithelial cell morphogenesis
maintenance of gastrointestinal epithelium

Cellular Component

plasma membrane
integral component of membrane
basolateral plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000415430
Coding exons: 8
Length: 34215
Individuals with no LoFs: 125712
Homozygous LoFs: 5
Heterozygous LoFs: 2
Defined: 125719
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.456	152	169	0.901	0.0000130	2763
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000074	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000073	0.000054	rare
Finnish	0.000063	0.000046	rare
European (Non-Finnish)	0.000012	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00045	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0750

Intolerance Scores

LoFtool: 0.482
RVIS EVS: -0.18
RVIS percentile EVS: 40.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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