GeneBe

ATP9A

protein-coding

ATPase phospholipid transporting 9A (putative), the group of ATPase phospholipid transporting

Gene summary

Enables protease binding activity. Involved in negative regulation of exosomal secretion; regulation of endocytic recycling; and regulation of retrograde transport, endosome to Golgi. Located in several cellular components, including endosome; perinuclear region of cytoplasm; and trans-Golgi network membrane. Implicated in neurodevelopmental disorder with poor growth and behavioral abnormalities. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006045.3

Inheritance

AR

ClinVar variants

P:13U:126B:28

Top phenotype

Neurodevelopmental disorder with poor growth and behavioral abnormalities

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr20:51,596,514-51,768,390

External References & Databases

Ensembl (ENSG00000054793)NCBI Gene (10079)OMIM (609126)HGNC:13540GenCCUniProt (O75110)AlphaFoldClinVar (ATP9A)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~171.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorder with poor growth and behavioral abnormalitiesSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859377

Submitter: Ambry Genetics

neurodevelopmental disorder with poor growth and behavioral abnormalitiesMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0859377

Submitter: G2P

neurodevelopmental disorder with poor growth and behavioral abnormalitiesSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859377

Submitter: PanelApp Australia

neurodevelopmental disorder with poor growth and behavioral abnormalitiesSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859377

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Neurodevelopmental disorder with poor growth and behavioral abnormalitiesAR

Manifestation: Craniofacial; Musculoskeletal; Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 34379057; 34764295; 36604604Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATP9A variants in ClinVar

5 Conditions Cataloged
Inborn genetic diseasesTotal: 101
not providedTotal: 39
Neurodevelopmental disorder with poor growth and behavioral abnormalitiesTotal: 15
not specifiedTotal: 12
See casesTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006045.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
23
clinvar
4
clinvar
 30
missense
117
clinvar
1
clinvar
 118
nonsense
5
clinvar
1
clinvar
2
clinvar
 8
start loss
0
frameshift
3
clinvar
 3
splice donor/acceptor (+/-2bp)
3
clinvar
1
clinvar
4
clinvar
 8
Total85126235167

Highest pathogenic variant AF is 0.0000034240993

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006045.3RefSeqNP_006036.128MANE Select
ENST00000338821.6EnsemblENSP00000342481.528MANE Select
ENST00000311637.10EnsemblENSP00000309086.523Standard
ENST00000311637.9EnsemblENSP00000309086.523Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ion channel transport
  • Transport of small molecules
  • Ion transport by P-type ATPases

Biological Process

  • retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
  • endocytosis
  • phospholipid translocation

Molecular Function

  • magnesium ion binding
  • phospholipid-translocating ATPase activity
  • ATP binding

Cellular Component

  • endosome
  • early endosome
  • trans-Golgi network
  • plasma membrane
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000338821
Coding exons
28
Length
172121
Individuals with no LoFs
125728
Homozygous LoFs
0
Heterozygous LoFs
20
Defined
125748
p
0.0000795
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense4.153476440.5390.00004156778
Missense (PolyPhen)87187.140.46491886
Synonymous-1.883132731.140.00001972072
Loss of Function6.62764.20.1090.00000354680

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish0.000300.00030rare
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000970.000097rare
South Asian0.0000660.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec
0.118

Intolerance Scores

LoFtool
0.104
RVIS EVS
-1.64
RVIS percentile EVS
2.8

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.217

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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