CD5

Chr 11

CD5 molecule

Also known as: LEU1, T1

NCBI Gene: 921 ENSG00000110448 UniProt: P06127 OMIM: 153340

CD5 encodes a transmembrane glycoprotein receptor that regulates T-cell and B-cell signaling, thymocyte selection, and immune tolerance by interacting with ligands like CD5L and CD72. Mutations cause autosomal dominant common variable immunodeficiency, resulting in recurrent infections due to antibody deficiency. The gene shows very low constraint against loss-of-function variants, consistent with a dominant inheritance pattern where one functional copy may be insufficient for normal immune function.

GeneReviews OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a member of the scavenger receptor cysteine-rich (SRCR) superfamily. Members of this family are secreted or membrane-anchored proteins mainly found in cells associated with the immune system. This protein is a type-I transmembrane glycoprotein found on the surface of thymocytes, T lymphocytes and a subset of B lymphocytes. The encoded protein contains three SRCR domains and may act as a receptor to regulate T-cell proliferation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2016]

GeneReviews OMIM ResearchGenerating clinical summary…

Active trials

482

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.03

LOEUF

Multiple*

Mechanism· predicted

📖

GeneReview available — CD5

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.03LOEUF

pLI 0.000

Z-score 1.44

OE 0.70 (0.49–1.03)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.96Z-score

OE missense 0.84 (0.76–0.94)

241 obs / 286.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.70 (0.49–1.03)

0≤0.351.4

Missense OE?0.84 (0.76–0.94)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 19 / 27.1Missense obs/exp: 241 / 286.8Syn Z: 0.32

Background carrier burden — how many people carry a rare variant somewhere in CD5?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 73

584 rare PASS variants

Rare truncating (LoF)

1 in 1,400

91 rare PASS variants

Rare synonymous (reference)

1 in 140

239 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CD5. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 89	1 in 1,200
South Asian	~43k	1 in 73	1 in 2,000
Remaining (unassigned)	~30k	1 in 64	1 in 2,500
European (Finnish)	~27k	1 in 300	1 in 2,600
Admixed American	~22k	1 in 69	1 in 4,200
African / African American	~21k	1 in 79	1 in 3,700
East Asian	~20k	1 in 77	1 in 1,400
Ashkenazi Jewish	~13k	1 in 410	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 96	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 10 coding exons well covered in gnomAD exomes and genomes.? see exons ↓