CD226

CD226 molecule, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 18:69831157-69961803

Links

ENSG00000150637 ∙ NCBI:10666 ∙ OMIM:605397 ∙ HGNC:16961 ∙ Uniprot:Q15762 ∙ 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 CD226 gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD226 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			9	3		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	3	0

Variants in CD226

This is a list of pathogenic ClinVar variants found in the CD226 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-69841334-C-T		not specified	Uncertain significance (Mar 31, 2022)
18-69841349-A-C		Inborn genetic diseases	Uncertain significance (Jan 31, 2023)
18-69841367-C-A		not specified	Uncertain significance (Jul 22, 2022)
18-69864415-T-C		not specified	Uncertain significance (Feb 13, 2024)
18-69864432-T-C		not specified	Uncertain significance (Oct 14, 2023)
18-69867394-C-T		not specified	Likely benign (Apr 25, 2023)
18-69873226-T-A		not specified	Uncertain significance (Mar 17, 2023)
18-69895752-C-T		not specified	Uncertain significance (Dec 08, 2023)
18-69895790-G-C		not specified	Uncertain significance (Aug 12, 2021)
18-69895797-C-T		not specified	Likely benign (Aug 12, 2021)
18-69895812-C-T		not specified	Uncertain significance (Jun 01, 2023)
18-69895919-G-A		not specified	Uncertain significance (Jan 09, 2024)
18-69895991-T-C		not specified	Uncertain significance (Nov 19, 2022)
18-69946766-G-A		not specified	Uncertain significance (Sep 14, 2023)
18-69946773-G-T		not specified	Uncertain significance (Jun 28, 2022)
18-69946859-A-G		not specified	Uncertain significance (Mar 02, 2023)
18-69946968-A-T		not specified	Uncertain significance (Feb 15, 2023)
18-69947025-C-T		not specified	Likely benign (Dec 21, 2022)
18-69947382-C-G		not specified	Uncertain significance (Nov 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD226	protein_coding	protein_coding	ENST00000280200	6	130646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0392	0.955	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.737	159	187	0.849	0.00000987	2196
Missense in Polyphen		31	51.332	0.60391		641
Synonymous	-0.184	73	71.0	1.03	0.00000443	635
Loss of Function	2.40	5	15.1	0.332	6.39e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000659	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in intercellular adhesion, lymphocyte signaling, cytotoxicity and lymphokine secretion mediated by cytotoxic T-lymphocyte (CTL) and NK cell (PubMed:8673704). Cell surface receptor for NECTIN2. Upon ligand binding, stimulates T- cell proliferation and cytokine production, including that of IL2, IL5, IL10, IL13, and IFNG. Competes with PVRIG for NECTIN2-binding (PubMed:26755705). {ECO:0000269|PubMed:26755705, ECO:0000269|PubMed:8673704}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.236

Intolerance Scores

• loftool: 0.469
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.19

Haploinsufficiency Scores

• pHI: 0.0647
• hipred: N
• hipred_score: 0.273
• ghis: 0.408

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd226
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; 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); hematopoietic system phenotype; neoplasm

Gene ontology

• Biological process: cytokine production;positive regulation of natural killer cell cytokine production;positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target;positive regulation of immunoglobulin mediated immune response;cell adhesion;signal transduction;cell recognition;positive regulation of interferon-gamma production;positive regulation of mast cell activation;positive regulation of natural killer cell mediated cytotoxicity;regulation of immune response;positive regulation of T cell receptor signaling pathway;positive regulation of Fc receptor mediated stimulatory signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;cell surface;membrane raft
• Molecular function: integrin binding;protein binding;protein kinase binding;cell adhesion molecule binding