ABCA1

Chr 9

ATP binding cassette subfamily A member 1

Also known as: ABC-1, ABC1, CERP, HDLCQTL13, HDLDT1, HPALP1, TGD

NCBI Gene: 19ENSG00000165029UniProt: O95477

The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. With cholesterol as its substrate, this protein functions as a cholesteral efflux pump in the cellular lipid removal pathway. Mutations in both alleles of this gene cause Tangier disease and familial high-density lipoprotein (HDL) deficiency. [provided by RefSeq, Sep 2019]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtTangier disease
UniProtHypoalphalipoproteinemia, primary, 1

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
2
Active trials
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Pubs (1 yr)
—
P/LP submissions
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P/LP missense
0.49
LOEUF
LOF
Mechanism· G2P
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GeneReview available — ABCA1
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?
0.49LOEUF
pLI 0.000
Z-score 6.23
OE 0.38 (0.30–0.49)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.75Z-score
OE missense 0.86 (0.81–0.90)
1029 obs / 1200.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.38 (0.30–0.49)
0≤0.351.4
Missense OE?0.86 (0.81–0.90)
0≤0.61.4
Synonymous OE?1.08
0≤1.21.6
LoF obs/exp: 44 / 116.5Missense obs/exp: 1029 / 1200.0Syn Z: -1.39

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

ABCA1 · protein map & ClinVar variants

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

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients