CD6

Chr 11

CD6 molecule

Also known as: TP120

NCBI Gene: 923ENSG00000013725UniProt: P30203

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]

119
ClinVar variants
10
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— CD6
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
10 Pathogenic / Likely Pathogenic· 88 VUS of 119 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.66LOEUF
pLI 0.000
Z-score 3.00
OE 0.40 (0.26–0.66)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.91Z-score
OE missense 0.71 (0.64–0.79)
253 obs / 354.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.40 (0.26–0.66)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.71 (0.64–0.79)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.93
0≤1.21.6
LoF obs/exp: 12 / 29.6Missense obs/exp: 253 / 354.1Syn Z: 0.69

ClinVar Variant Classifications

119 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic6
Likely Pathogenic4
VUS88
Likely Benign9
Benign12
6
Pathogenic
4
Likely Pathogenic
88
VUS
9
Likely Benign
12
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
6
0
6
Likely Pathogenic
0
0
4
0
4
VUS
0
85
3
0
88
Likely Benign
0
5
0
4
9
Benign
0
5
2
5
12
Total095159119

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CD6 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
CD6 ANTIGEN; CD6
MIM #186720 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Single-cell RNA-sequencing and spatial transcriptomic analysis reveal a distinct population of APOE(-) cells yielding pathological lymph node metastasis in papillary thyroid cancer.
Xiao G et al.·Clin Transl Med
2025
Clinical and experimental evidence for targeting CD6 in immune-based disorders.
Consuegra-Fernández M et al.·Autoimmun Rev
2018Review
The Link Between CD6 and Autoimmunity: Genetic and Cellular Associations.
Kofler DM et al.·Curr Drug Targets
2016Review
Tolerance and chimerism.
Kolb HJ et al.·Transplantation
2003Review
CD6 as a Cell Surface Receptor and As a Target for Regulating Immune Responses.
Brown MH·Curr Drug Targets
2016Review
New Targeted Therapies for Uncontrolled Asthma.
Corren J·J Allergy Clin Immunol Pract
2019Review
CD6 as a therapeutic target in autoimmune diseases: successes and challenges.
Pinto M et al.·BioDrugs
2013Review
Association between circulating inflammatory proteins and benign prostatic disease: a Mendelian randomization study.
Cao H et al.·Sci Rep
2024
Therapeutic Targeting of CD6 in Autoimmune Diseases: A Review of Cuban Clinical Studies with the Antibodies IOR-T1 and Itolizumab.
Hernández P et al.·Curr Drug Targets
2016Review
Lipid metabolism-related gene signature predicts prognosis and unveils novel anti-tumor drugs in specific type of diffuse large B cell lymphoma.
Wang C et al.·Mol Med
2024
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
ALCAM-CD6 axis suppression: a key determinant of immune-mediated metastasis recurrence in stage III non-small cell lung cancer.
Wen S et al.·J Immunother Cancer
2025🔓 Open Access
Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway.
Juric I et al.·NPJ Precis Oncol
2025🔓 Open Access
CD6 expression is an independent predictor of time to first treatment in chronic lymphocytic leukemia.
Carrillo-Serradell L et al.·Haematologica
2026
The OT-II model reveals dual in vitro and in vivo immunomodulatory properties of CD6 in T cell activation.
Leyton-Pereira A et al.·Front Immunol
2025🔓 Open AccessFunctional
Pediatric Atopic Dermatitis Exhibits Distinctive Patterns in JAK/STAT Pathway Activation and CD6-ALCAM Signaling.
Jeong S et al.·Immune Netw
2025🔓 Open Access
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools