CD1A

Chr 1

CD1a molecule

Also known as: CD1, FCB6, HTA1, R4, T6

NCBI Gene: 909 ENSG00000158477 UniProt: P06126 OMIM: 188370

This gene encodes a member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to the plasma membrane and to recycling vesicles of the early endocytic system. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.95

Clinical Summary— CD1A

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

50 VUS of 64 total submissions

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Clinical Trials

2 active or recruiting trials — potential therapeutic options may be available

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.95LOEUF

pLI 0.000

Z-score -2.50

OE 1.64 (1.20–1.95)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.61Z-score

OE missense 1.12 (1.00–1.26)

215 obs / 191.2 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.64 (1.20–1.95)

0≤0.351.4

Missense OE?1.12 (1.00–1.26)

0≤0.61.4

Synonymous OE?1.15

0≤1.21.6

LoF obs/exp: 29 / 17.7Missense obs/exp: 215 / 191.2Syn Z: -1.01

This gene — mechanism propensity

0.75top 25%

GOF

0.6151th %ile

LOF

0.2287th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

64 submitted variants in ClinVar

ClinVar

Classification Summary

VUS50

Likely Benign9

Benign2

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	50	0	0	50
Likely Benign	8	0	1	9
Benign	1	1	0	2
Total	59	1	1	61

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

View in ClinVar →

10 pathogenic / likely-pathogenic (of 12) ClinVar copy-number / structural variants overlap CD1A — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →