CD6

CD6 molecule, the group of CD molecules|Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 11:60971679-61020377

Links

ENSG00000013725 ∙ NCBI:923 ∙ OMIM:186720 ∙ HGNC:1691 ∙ Uniprot:P30203 ∙ 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 CD6 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD6 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	23	0	0

Variants in CD6

This is a list of pathogenic ClinVar variants found in the CD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-60971922-C-T		CD6-related disorder	Benign (Aug 20, 2019)
11-61006589-C-A		not specified	Uncertain significance (Aug 30, 2022)
11-61006628-A-T		not specified	Uncertain significance (Nov 21, 2023)
11-61007670-C-A		not specified	Uncertain significance (Jun 06, 2023)
11-61007755-C-G		not specified	Uncertain significance (Jul 05, 2023)
11-61007757-C-G		not specified	Uncertain significance (Sep 06, 2022)
11-61007802-C-G		not specified	Uncertain significance (Dec 18, 2023)
11-61008546-T-G		not specified	Uncertain significance (Oct 03, 2023)
11-61008560-G-C		not specified	Uncertain significance (Nov 22, 2023)
11-61008631-T-C		CD6-related disorder	Benign (Nov 01, 2019)
11-61008698-C-T		not specified	Uncertain significance (Jun 02, 2023)
11-61008714-C-T		CD6-related disorder	Benign (Oct 22, 2019)
11-61008737-C-T		CD6-related disorder	Benign (Oct 17, 2019)
11-61008834-C-T		CD6-related disorder	Benign (Sep 24, 2019)
11-61008835-G-C		CD6-related disorder	Benign (Nov 01, 2019)
11-61009576-C-A		not specified	Uncertain significance (Dec 19, 2022)
11-61009601-G-A		CD6-related disorder	Benign (Dec 03, 2019)
11-61009722-C-A		not specified	Uncertain significance (Apr 07, 2022)
11-61009733-C-A		not specified	Uncertain significance (Jul 26, 2022)
11-61009737-A-G		not specified	Uncertain significance (Apr 28, 2022)
11-61009767-T-C		not specified	Uncertain significance (Jul 19, 2022)
11-61009773-A-T		not specified	Uncertain significance (Jun 21, 2023)
11-61011105-G-A		not specified	Uncertain significance (Oct 14, 2023)
11-61013472-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-61013491-G-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD6	protein_coding	protein_coding	ENST00000313421	13	48735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000927	0.999	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.91	253	354	0.715	0.0000196	4256
Missense in Polyphen		69	123.43	0.55904		1525
Synonymous	0.695	144	155	0.929	0.00000970	1344
Loss of Function	3.00	12	29.6	0.405	0.00000135	349

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000363	0.000358
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000111	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell adhesion molecule that mediates cell-cell contacts and regulates T-cell responses via its interaction with ALCAM/CD166 (PubMed:15048703, PubMed:15294938, PubMed:16352806, PubMed:16914752, PubMed:24945728, PubMed:24584089). Contributes to signaling cascades triggered by activation of the TCR/CD3 complex (PubMed:24584089). Functions as costimulatory molecule; promotes T-cell activation and proliferation (PubMed:15294938, PubMed:16352806, PubMed:16914752). Contributes to the formation and maturation of the immunological synapse (PubMed:15294938, PubMed:16352806). Functions as calcium-dependent pattern receptor that binds and aggregates both Gram-positive and Gram-negative bacteria. Binds both lipopolysaccharide (LPS) from Gram-negative bacteria and lipoteichoic acid from Gram-positive bacteria (PubMed:17601777). LPS binding leads to the activation of signaling cascades and down-stream MAP kinases (PubMed:17601777). Mediates activation of the inflammatory response and the secretion of pro-inflammatory cytokines in response to LPS (PubMed:17601777). {ECO:0000269|PubMed:15048703, ECO:0000269|PubMed:15294938, ECO:0000269|PubMed:16352806, ECO:0000269|PubMed:16914752, ECO:0000269|PubMed:17601777, ECO:0000269|PubMed:24584089, ECO:0000269|PubMed:24945728}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.584
• rvis_EVS: 0.82
• rvis_percentile_EVS: 88.02

Haploinsufficiency Scores

• pHI: 0.242
• hipred: Y
• hipred_score: 0.542
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.567

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd6
• Phenotype: hematopoietic system phenotype; homeostasis/metabolism phenotype; immune system phenotype

Gene ontology

• Biological process: immunological synapse formation;adaptive immune response;acute inflammatory response to antigenic stimulus;receptor-mediated endocytosis;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;lipopolysaccharide-mediated signaling pathway;response to lipopolysaccharide;positive regulation of T cell proliferation;innate immune response;positive regulation of cytokine production involved in inflammatory response
• Cellular component: immunological synapse;extracellular region;integral component of plasma membrane;external side of plasma membrane;intrinsic component of plasma membrane;T cell receptor complex
• Molecular function: lipopolysaccharide binding;scavenger receptor activity;protein binding;identical protein binding;lipoteichoic acid binding