VSIG4

V-set and immunoglobulin domain containing 4, the group of Complement system regulators and receptors|V-set domain containing

Basic information

Region (hg38): X:66021738-66040125

Links

ENSG00000155659 ∙ NCBI:11326 ∙ OMIM:300353 ∙ HGNC:17032 ∙ Uniprot:Q9Y279 ∙ 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 VSIG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSIG4 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		3
missense			19	3	4	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4		4
non coding				2	1	3
Total	0	0	19	8	5

Variants in VSIG4

This is a list of pathogenic ClinVar variants found in the VSIG4 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-66022136-G-A		VSIG4-related disorder	Likely benign (Aug 01, 2019)
X-66022277-T-G		VSIG4-related disorder	Uncertain significance (May 09, 2024)
X-66022288-G-T		not specified	Uncertain significance (Mar 02, 2023)
X-66022315-G-A			Benign (May 08, 2018)
X-66022328-G-A		not specified	Uncertain significance (Oct 25, 2022)
X-66022331-C-T		not specified	Uncertain significance (Jan 04, 2022)
X-66022433-A-G		not specified	Likely benign (May 14, 2024)
X-66022856-A-G		not specified	Uncertain significance (Oct 24, 2023)
X-66025082-A-G		not specified	Uncertain significance (May 02, 2024)
X-66027490-G-A		not specified	Uncertain significance (Mar 20, 2023)
X-66027491-T-A		not specified	Uncertain significance (Sep 02, 2021)
X-66027520-G-C		not specified	Uncertain significance (Feb 27, 2024)
X-66027533-A-G			Likely benign (Feb 01, 2023)
X-66028042-A-G		VSIG4-related disorder	Likely benign (Oct 07, 2019)
X-66028071-T-A		not specified	Uncertain significance (Apr 12, 2024)
X-66028077-G-C		not specified	Uncertain significance (Nov 21, 2022)
X-66028085-G-A		not specified	Uncertain significance (Dec 17, 2021)
X-66028109-G-A		not specified	Uncertain significance (Jan 03, 2024)
X-66032461-C-T			Likely benign (Apr 10, 2018)
X-66032493-G-A		VSIG4-related disorder	Likely benign (Mar 06, 2019)
X-66032493-G-T		not specified	Uncertain significance (Sep 16, 2021)
X-66032518-C-T			Uncertain significance (-)
X-66032549-C-T		not specified	Uncertain significance (Jul 13, 2021)
X-66032559-C-T		VSIG4-related disorder	Likely benign (Jul 15, 2019)
X-66032572-A-T		VSIG4-related disorder	Likely benign (Dec 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSIG4	protein_coding	protein_coding	ENST00000374737	8	18388

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.50e-9	0.0610	125587	26	48	125661	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.43	208	158	1.32	0.0000123	2584
Missense in Polyphen		43	42.333	1.0158		783
Synonymous	-1.62	78	61.8	1.26	0.00000482	802
Loss of Function	-0.263	13	12.0	1.08	8.45e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000366	0.0000366
Ashkenazi Jewish	0.00	0.00
East Asian	0.000385	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000771	0.000537
Middle Eastern	0.000385	0.000272
South Asian	0.000273	0.000163
Other	0.000447	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phagocytic receptor, strong negative regulator of T-cell proliferation and IL2 production. Potent inhibitor of the alternative complement pathway convertases. {ECO:0000269|PubMed:17016562, ECO:0000269|PubMed:17051150}.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Human Complement System (Consensus)

Recessive Scores

• pRec: 0.0965

Intolerance Scores

• loftool: 0.888
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.241
• hipred: N
• hipred_score: 0.123
• ghis: 0.385

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.151

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vsig4
• Phenotype: immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype

Gene ontology

• Biological process: complement activation, alternative pathway;negative regulation of interleukin-2 production;negative regulation of T cell proliferation;negative regulation of macrophage activation
• Cellular component: integral component of membrane