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CD6 CD6 molecule [ Homo sapiens (human) ]

Gene ID: 923, updated on 15-Oct-2023

Summary

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Official Symbol
CD6provided by HGNC
Official Full Name
CD6 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1691
See related
Ensembl:ENSG00000013725 MIM:186720; AllianceGenome:HGNC:1691
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TP120
Summary
This gene encodes a protein found on the outer membrane of T-lymphocytes as well as some other immune cells. The encoded protein contains three scavenger receptor cysteine-rich (SRCR) domains and a binding site for an activated leukocyte cell adhesion molecule. The gene product is important for continuation of T cell activation. This gene may be associated with susceptibility to multiple sclerosis (PMID: 19525953, 21849685). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
Expression
Biased expression in lymph node (RPKM 22.7), appendix (RPKM 13.7) and 9 other tissues See more
Orthologs
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Genomic context

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See CD6 in Genome Data Viewer
Location:
11q12.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (60971680..61020377)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (60922811..60971572)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (60739152..60787849)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902676 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:60686309-60687508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3379 Neighboring gene transmembrane protein 109 Neighboring gene transmembrane protein 132A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4786 Neighboring gene solute carrier family 15 member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3381 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4788 Neighboring gene RNA, U6 small nuclear 933, pseudogene Neighboring gene tRNA-Ala (TGC) 10-1 Neighboring gene uncharacterized LOC105369326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:60774736-60775444 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:60779887-60780476 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:60780477-60781066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:60793655-60794220 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3384 Neighboring gene uncharacterized LOC105369325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:60824202-60824702 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:60828388-60829587 Neighboring gene long intergenic non-protein coding RNA 2954 Neighboring gene uncharacterized LOC124902677

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Th1 and Th17 cells are resistant towards T cell activation-induced downregulation of CD6. Brück C, et al. Clin Immunol, 2022 May. PMID 35487454
  2. Compromised levels of CD6 and reduced T cell activation in the aged immune system. Kureel AK, et al. Biomarkers, 2021 Jul. PMID 33913383
  3. The Link Between CD6 and Autoimmunity: Genetic and Cellular Associations. Kofler DM, et al. Curr Drug Targets, 2016. PMID 26844569
  4. CD6 as a Cell Surface Receptor and As a Target for Regulating Immune Responses. Brown MH. Curr Drug Targets, 2016. PMID 26302795
  5. Tuning T Cell Activation: The Function of CD6 At the Immunological Synapse and in T Cell Responses. Santos RF, et al. Curr Drug Targets, 2016. PMID 26028048

See all (67) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Gene variation impact on prostate cancer progression: Lymphocyte modulator, activation, and cell adhesion gene variant contribution.
    Title: Gene variation impact on prostate cancer progression: Lymphocyte modulator, activation, and cell adhesion gene variant contribution.
  2. Th1 and Th17 cells are resistant towards T cell activation-induced downregulation of CD6.
    Title: Th1 and Th17 cells are resistant towards T cell activation-induced downregulation of CD6.
  3. The CD6/ALCAM pathway promotes lupus nephritis via T cell-mediated responses.
    Title: The CD6/ALCAM pathway promotes lupus nephritis via T cell-mediated responses.
  4. Compromised levels of CD6 and reduced T cell activation in the aged immune system.
    Title: Compromised levels of CD6 and reduced T cell activation in the aged immune system.
  5. Contribution of Evolutionary Selected Immune Gene Polymorphism to Immune-Related Disorders: The Case of Lymphocyte Scavenger Receptors CD5 and CD6.
    Title: Contribution of Evolutionary Selected Immune Gene Polymorphism to Immune-Related Disorders: The Case of Lymphocyte Scavenger Receptors CD5 and CD6.
  6. Attenuation of Murine Collagen-Induced Arthritis by Targeting CD6.
    Title: Attenuation of Murine Collagen-Induced Arthritis by Targeting CD6.
  7. these results provide new supportive evidence of the contribution of the CD6 lymphocyte receptor in psoriasis at both experimental and clinical levels.
    Title: Genetic and experimental evidence for the involvement of the CD6 lymphocyte receptor in psoriasis.
  8. These data indicate that overexpression of CD6 and ALCAM in the inflamed mucosa of IBD patients accelerates intestinal mucosal immune responses via promoting CD4+ T cell proliferation and differentiation into Th1/Th17 cells.
    Title: Critical Role of CD6highCD4+ T Cells in Driving Th1/Th17 Cell Immune Responses and Mucosal Inflammation in IBD.
  9. This study provides evidence that CD6 is involved in the susceptibility to Behcet's disease in a Chinese Han population.
    Title: Genetic polymorphisms of cell adhesion molecules in Behcet's disease in a Chinese Han population.
  10. These results suggest that (i) CD6 is a negative regulator of T-cell activation, (ii) at the same time, CD6 is a positive regulator of activated T-cell survival/proliferation and infiltration; and (iii) CD6 is a potential new target for treating multiple sclerosis (MS)and potentially other T-cell-driven autoimmune conditions.
    Title: CD6 as a potential target for treating multiple sclerosis.
Submit: New GeneRIF Correction See all GeneRIFs (43)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci.
EBI GWAS Catalog
Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ44171

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables lipopolysaccharide binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables lipoteichoic acid binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in acute inflammatory response to antigenic stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in adaptive immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in immunological synapse formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in lipopolysaccharide-mediated signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of T cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cytokine production involved in inflammatory response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of protein phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in response to lipopolysaccharide IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of T cell receptor complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cell surface IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in immunological synapse IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
T-cell differentiation antigen CD6
Names
CD6 antigen
T12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001254750.2 → NP_001241679.1  T-cell differentiation antigen CD6 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001241679.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 3' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
    Source sequence(s)
    AI657093, AP003721, U66145
    Consensus CDS
    CCDS58138.1
    UniProtKB/TrEMBL
    Q8N4Q7
    Related
    ENSP00000340628.5, ENST00000352009.9
    Conserved Domains (2) summary
    smart00202
    Location:161 → 260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166 → 260
    SRCR; Scavenger receptor cysteine-rich domain

  2. NM_001254751.2 → NP_001241680.1  T-cell differentiation antigen CD6 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001241680.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.
    Source sequence(s)
    AI657093, AP003721, U66146
    Consensus CDS
    CCDS58137.1
    UniProtKB/TrEMBL
    Q8N4Q7
    Related
    ENSP00000390676.2, ENST00000452451.6
    Conserved Domains (2) summary
    smart00202
    Location:161 → 260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166 → 260
    SRCR; Scavenger receptor cysteine-rich domain

  3. NM_006725.5 → NP_006716.3  T-cell differentiation antigen CD6 isoform 1 precursor

    See identical proteins and their annotated locations for NP_006716.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
    Source sequence(s)
    BC033755, BC078669, DB155411
    Consensus CDS
    CCDS7999.1
    UniProtKB/Swiss-Prot
    A4KAD4, A4KAD5, P30203, Q8WWJ3, Q8WWJ4, Q8WWJ5, Q8WWJ6, Q8WWJ7, Q9UMF2, Q9Y4K7, Q9Y4K8, Q9Y4K9, Q9Y4L0
    UniProtKB/TrEMBL
    A8K9I9
    Related
    ENSP00000323280.7, ENST00000313421.11
    Conserved Domains (2) summary
    smart00202
    Location:161 → 260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166 → 260
    SRCR; Scavenger receptor cysteine-rich domain

RNA

  1. NR_045638.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in an internal exon and lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI657093, AP003721, DB155411, X60992
    Related
    ENST00000344931.9

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    60971680..61020377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427881.1 → XP_047283837.1  T-cell differentiation antigen CD6 isoform X13

  2. XM_011545360.3 → XP_011543662.1  T-cell differentiation antigen CD6 isoform X1

    UniProtKB/TrEMBL
    A8K9I9
    Conserved Domains (2) summary
    smart00202
    Location:161 → 260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166 → 260
    SRCR; Scavenger receptor cysteine-rich domain

  3. XM_047427875.1 → XP_047283831.1  T-cell differentiation antigen CD6 isoform X4

    UniProtKB/TrEMBL
    Q8N4Q7

  4. XM_006718739.3 → XP_006718802.1  T-cell differentiation antigen CD6 isoform X5

    UniProtKB/TrEMBL
    A8K9I9
    Conserved Domains (2) summary
    smart00202
    Location:161 → 260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166 → 260
    SRCR; Scavenger receptor cysteine-rich domain

  5. XM_006718740.3 → XP_006718803.1  T-cell differentiation antigen CD6 isoform X6

    UniProtKB/TrEMBL
    A8K9I9
    Conserved Domains (2) summary
    smart00202
    Location:161 → 260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166 → 260
    SRCR; Scavenger receptor cysteine-rich domain

  6. XM_006718738.3 → XP_006718801.1  T-cell differentiation antigen CD6 isoform X2

    UniProtKB/TrEMBL
    A8K9I9
    Conserved Domains (2) summary
    smart00202
    Location:161 → 260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166 → 260
    SRCR; Scavenger receptor cysteine-rich domain

  7. XM_047427874.1 → XP_047283830.1  T-cell differentiation antigen CD6 isoform X3

    UniProtKB/TrEMBL
    A8K9I9

  8. XM_011545362.3 → XP_011543664.1  T-cell differentiation antigen CD6 isoform X7

    UniProtKB/TrEMBL
    A8K9I9
    Conserved Domains (2) summary
    smart00202
    Location:161 → 260
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:166 → 260
    SRCR; Scavenger receptor cysteine-rich domain

  9. XM_047427876.1 → XP_047283832.1  T-cell differentiation antigen CD6 isoform X8

    UniProtKB/TrEMBL
    A8K9I9

  10. XM_047427879.1 → XP_047283835.1  T-cell differentiation antigen CD6 isoform X11

    UniProtKB/TrEMBL
    Q8N4Q7

  11. XM_047427880.1 → XP_047283836.1  T-cell differentiation antigen CD6 isoform X12

  12. XM_047427877.1 → XP_047283833.1  T-cell differentiation antigen CD6 isoform X9

    UniProtKB/TrEMBL
    A8K9I9

  13. XM_047427878.1 → XP_047283834.1  T-cell differentiation antigen CD6 isoform X10

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    60922811..60971572
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370518.1 → XP_054226493.1  T-cell differentiation antigen CD6 isoform X1

    UniProtKB/TrEMBL
    A8K9I9

  2. XM_054370521.1 → XP_054226496.1  T-cell differentiation antigen CD6 isoform X4

    UniProtKB/TrEMBL
    Q8N4Q7

  3. XM_054370522.1 → XP_054226497.1  T-cell differentiation antigen CD6 isoform X5

    UniProtKB/TrEMBL
    A8K9I9

  4. XM_054370523.1 → XP_054226498.1  T-cell differentiation antigen CD6 isoform X6

    UniProtKB/TrEMBL
    A8K9I9

  5. XM_054370519.1 → XP_054226494.1  T-cell differentiation antigen CD6 isoform X2

    UniProtKB/TrEMBL
    A8K9I9

  6. XM_054370520.1 → XP_054226495.1  T-cell differentiation antigen CD6 isoform X3

    UniProtKB/TrEMBL
    A8K9I9

  7. XM_054370524.1 → XP_054226499.1  T-cell differentiation antigen CD6 isoform X7

    UniProtKB/TrEMBL
    A8K9I9

  8. XM_054370525.1 → XP_054226500.1  T-cell differentiation antigen CD6 isoform X8

    UniProtKB/TrEMBL
    A8K9I9

  9. XM_054370528.1 → XP_054226503.1  T-cell differentiation antigen CD6 isoform X11

    UniProtKB/TrEMBL
    Q8N4Q7

  10. XM_054370529.1 → XP_054226504.1  T-cell differentiation antigen CD6 isoform X12

  11. XM_054370526.1 → XP_054226501.1  T-cell differentiation antigen CD6 isoform X9

    UniProtKB/TrEMBL
    A8K9I9

  12. XM_054370527.1 → XP_054226502.1  T-cell differentiation antigen CD6 isoform X10

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P30203.3 GenPept UniProtKB/Swiss-Prot:P30203

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