ABCA13

Chr 7

ATP binding cassette subfamily A member 13

NCBI Gene: 154664ENSG00000179869UniProt: Q86UQ4

May mediate the cholesterol and gangliosides transport from the plasma membrane to intracellular vesicles in an ATP hydrolysis dependent manner, thus playing a role in their internalization by endocytic retrograde transport and may also participate in the endocytosis of synaptic vesicle in cortical neurons

547
ClinVar variants
2
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— ABCA13
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
2 Pathogenic / Likely Pathogenic· 452 VUS of 547 total submissions

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.
1.03LOEUF
pLI 0.000
Z-score 1.11
OE 0.92 (0.81–1.03)
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.
-1.52Z-score
OE missense 1.09 (1.05–1.12)
2662 obs / 2450.0 exp
Tolerant

Tolerant to missense variation

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.0.92 (0.81–1.03)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.09 (1.05–1.12)
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.1.04
0≤1.21.6
LoF obs/exp: 183 / 199.9Missense obs/exp: 2662 / 2450.0Syn Z: -1.00

ClinVar Variant Classifications

547 submitted variants in ClinVar

ClinVar

Classification Summary

Likely Pathogenic2
VUS452
Likely Benign78
Benign13
Conflicting2
2
Likely Pathogenic
452
VUS
78
Likely Benign
13
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
0
0
0
Likely Pathogenic
1
0
1
0
2
VUS
5
444
3
0
452
Likely Benign
1
56
0
21
78
Benign
0
11
1
1
13
Conflicting
—2
Total7511522547

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

View in ClinVar →

Protein Context — Lollipop Plot

ABCA13 · 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 Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Whole-Exome Sequencing Among Chinese Patients With Hereditary Diffuse Gastric Cancer.
Liu ZX et al.·JAMA Netw Open
2022Cohort
ATP-binding cassette transporter 13 mRNA expression level in schizophrenia patients.
Qian L et al.·Sci Rep
2020Cohort
Involvement of Rare Mutations of SCN9A, DPP4, ABCA13, and SYT14 in Schizophrenia and Bipolar Disorder.
Chen CH et al.·Int J Mol Sci
2021
CIAPIN1 and ABCA13 are markers of poor survival in metastatic ovarian serous carcinoma.
Nymoen DA et al.·Mol Cancer
2015
Association between the variability of the ABCA13 gene and the risk of major depressive disorder and schizophrenia in the Han Chinese population.
Chen J et al.·World J Biol Psychiatry
2017
Lipidomics and genomics in mental health: insights into major depressive disorder, bipolar disorder, schizophrenia, and obsessive-compulsive disorder.
Modesti MN et al.·Lipids Health Dis
2025
The association of ABC proteins with multidrug resistance in cancer.
Marques AVL et al.·Biochim Biophys Acta Mol Cell Res
2025Review
A cytogenetic abnormality and rare coding variants identify ABCA13 as a candidate gene in schizophrenia, bipolar disorder, and depression.
Knight HM et al.·Am J Hum Genet
2009
Rectal cancer sub-clones respond differentially to neoadjuvant therapy.
Frydrych LM et al.·Neoplasia
2019
Preliminary radiogenomic study of hepatitis B virus-related hepatocellular carcinoma: associations between MRI features and mutations.
Gao S et al.·Per Med
2023
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools