ABCA9

Chr 17

ATP binding cassette subfamily A member 9

Also known as: EST640918

NCBI Gene: 10350UniProt: Q8IUA7

This gene is a member of the superfamily of ATP-binding cassette (ABC) transporters and the encoded protein contains two transmembrane domains and two nucleotide binding folds. 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, and White). This gene is a member of the ABC1 subfamily and is clustered with four other ABC1 family members on chromosome 17q24. Transcriptional expression of this gene is induced during monocyte differentiation into macrophages and is suppressed by cholesterol import. [provided by RefSeq, Jul 2008]

0
Active trials
11
Pathogenic / LP
239
ClinVar variants
1
Pubs (1 yr)
0.8
Missense Z
1.07
LOEUF
Clinical Summary— ABCA9
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
11 Pathogenic / Likely Pathogenic· 207 VUS of 239 total submissions
Some data sources returned errors (1)

ensembl: TimeoutError: The operation was aborted due to timeout

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.
1.07LOEUF
pLI 0.000
Z-score 0.99
OE 0.89 (0.74–1.07)
Tolerant

Highly tolerant — LoF variants common in population

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.
0.75Z-score
OE missense 0.93 (0.87–0.98)
766 obs / 826.8 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.0.89 (0.74–1.07)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.93 (0.87–0.98)
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.0.97
0≤1.21.6
LoF obs/exp: 78 / 88.0Missense obs/exp: 766 / 826.8Syn Z: 0.48

ClinVar Variant Classifications

239 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic10
Likely Pathogenic1
VUS207
Likely Benign21
10
Pathogenic
1
Likely Pathogenic
207
VUS
21
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
10
0
10
Likely Pathogenic
0
0
1
0
1
VUS
0
202
5
0
207
Likely Benign
0
13
1
7
21
Benign
0
0
0
0
0
Total0215177239

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

View in ClinVar →

Protein Context — Lollipop Plot

ABCA9 · 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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Involvement of ABC transporters in melanogenesis and the development of multidrug resistance of melanoma.
Chen KG et al.·Pigment Cell Melanoma Res
2009Review
ABCA transporter gene expression and poor outcome in epithelial ovarian cancer.
Hedditch EL et al.·J Natl Cancer Inst
2014
Establishment of a prognostic signature for lung adenocarcinoma using cuproptosis-related lncRNAs.
Yalimaimaiti S et al.·BMC Bioinformatics
2023
Early Transcriptional Changes of Adipose-Derived Stem Cells (ADSCs) in Cell Culture.
Taha S et al.·Medicina (Kaunas)
2022
Gene expression of membrane transporters: Importance for prognosis and progression of ovarian carcinoma.
Elsnerova K et al.·Oncol Rep
2016
Integrative analysis of mRNA and miRNA expression profiles and somatic variants in oxysterol signaling in early-stage luminal breast cancer.
Holý P et al.·Mol Oncol
2023
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Increased expression of fatty acid and ABC transporters enhances seed oil production in camelina
Cai G et al.·Biotechnol Biofuels
2021
Chromosomal Rearrangements Identified in Three Additional Patients With Generalized Congenital Hypertrichosis With Gingival Hyperplasia Involving the 17q24.2-q24.3 Locus.
Tenorio-Castano J et al.·Clin Genet
2026Cohort
Expression analysis of PPAR-related lncRNAs in breast cancer.
Ghafouri-Fard S et al.·Pathol Res Pract
2023
Comprehensive Analysis of ABCA Family Members in Lung Adenocarcinoma with Prognostic Values.
Yang Y et al.·Mol Biotechnol
2022
Genome-Wide Association Study for Somatic Skeletal Traits in Duroc x (Landrace x Yorkshire) Pigs
Gao X et al.·Animals (Basel)
2023
ATP-binding cassette transporter expression is widely dysregulated in frontotemporal dementia with TDP-43 inclusions
Katzeff JS et al.·Front Mol Neurosci
2022
Top 6 full-text resultsSearch PubTator3 ↗

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