CRTAM

Chr 11

cytotoxic and regulatory T cell molecule

Also known as: CD355

NCBI Gene: 56253 ENSG00000109943 UniProt: O95727 OMIM: 612597

The CRTAM gene is upregulated in CD4 (see MIM 186940)-positive and CD8 (see CD8A; MIM 186910)-positive T cells and encodes a type I transmembrane protein with V and C1-like Ig domains (Yeh et al., 2008 [PubMed 18329370]).[supplied by OMIM, Feb 2009]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.17

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.17LOEUF

pLI 0.000

Z-score 1.00

OE 0.76 (0.51–1.17)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.37Z-score

OE missense 0.93 (0.82–1.04)

189 obs / 204.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.76 (0.51–1.17)

0≤0.351.4

Missense OE?0.93 (0.82–1.04)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 15 / 19.8Missense obs/exp: 189 / 204.0Syn Z: 0.00

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

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 95

499 rare PASS variants

Rare truncating (LoF)

1 in 1,500

90 rare PASS variants

Rare synonymous (reference)

1 in 200

174 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CRTAM. 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 150	1 in 1,800
South Asian	~43k	1 in 120	1 in 830
Remaining (unassigned)	~30k	1 in 130	1 in 1,400
European (Finnish)	~27k	1 in 480	1 in 1,900
Admixed American	~22k	1 in 140	1 in 2,000
African / African American	~21k	1 in 93	1 in 660
East Asian	~20k	1 in 210	1 in 1,600
Ashkenazi Jewish	~13k	1 in 1,000	1 in 1,000
Middle Eastern	~2,884	1 in 86	≈ 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): 9 of 10 coding exons well covered in gnomAD exomes; exon 6 marginal. Genomes: all 10.? see exons ↓