ATP10A

Chr 15

ATPase phospholipid transporting 10A (putative)

Also known as: ATP10C, ATPVA, ATPVC

NCBI Gene: 57194ENSG00000206190UniProt: O60312

The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. This gene is maternally expressed. It maps within the most common interval of deletion responsible for Angelman syndrome, also known as 'happy puppet syndrome'. [provided by RefSeq, Jul 2008]

683
ClinVar variants
310
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— ATP10A
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.28) despite low pLI — interpret in context.
📋
ClinVar Variants
310 Pathogenic / Likely Pathogenic· 245 VUS of 683 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
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.
0.43LOEUF
pLI 0.002
Z-score 5.12
OE 0.28 (0.19–0.43)
Moderately constrained

More LoF-intolerant than ~75% of genes

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.
0.76Z-score
OE missense 0.93 (0.88–0.98)
824 obs / 887.7 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.0.28 (0.19–0.43)
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 (0.88–0.98)
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.1.00
0≤1.21.6
LoF obs/exp: 17 / 59.7Missense obs/exp: 824 / 887.7Syn Z: 0.00

ClinVar Variant Classifications

683 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic302
Likely Pathogenic8
VUS245
Likely Benign64
Benign33
Conflicting2
302
Pathogenic
8
Likely Pathogenic
245
VUS
64
Likely Benign
33
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
302
0
302
Likely Pathogenic
0
0
8
0
8
VUS
1
240
4
0
245
Likely Benign
0
26
7
31
64
Benign
0
16
3
14
33
Conflicting
—2
Total128232445654

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

View in ClinVar →

Protein Context — Lollipop Plot

ATP10A · 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
Substrates of P4-ATPases: beyond aminophospholipids (phosphatidylserine and phosphatidylethanolamine).
Shin HW et al.·FASEB J
2019Review
Meta-Analyses Support Previous and Novel Autism Candidate Genes: Outcomes of an Unexplored Brazilian Cohort.
da Silva Montenegro EM et al.·Autism Res
2020Meta-analysis
Role of UBE3A and ATP10A genes in autism susceptibility region 15q11-q13 in an Italian population: a positive replication for UBE3A.
Guffanti G et al.·Psychiatry Res
2011
Genome-Wide DNA Methylation Profiles of Phlegm-Dampness Constitution.
Yao H et al.·Cell Physiol Biochem
2018
Integrated Analysis of Coexpression and Exome Sequencing to Prioritize Susceptibility Genes for Familial Cutaneous Melanoma.
Yepes S et al.·J Invest Dermatol
2022
Machine Learning for the Identification of a Common Signature for Anti-SSA/Ro 60 Antibody Expression Across Autoimmune Diseases.
Foulquier N et al.·Arthritis Rheumatol
2022
Genome-wide DNA methylation profiling identifies two novel genes in cervical neoplasia.
El-Zein M et al.·Int J Cancer
2020
Exploring Neuronal Vulnerability to Head Trauma Using a Whole Exome Approach.
Ibrahim O et al.·J Neurotrauma
2020
Genome-scale network analysis of imprinted human metabolic genes.
Sigurdsson MI et al.·Epigenetics
2009Review
Methylation markers for anal cancer screening: A repeated cross-sectional analysis of people living with HIV, 2015-2016.
Vasavada A et al.·Int J Cancer
2024
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