ATP9A ATPase phospholipid transporting 9A (putative) [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATP9Aprovided by HGNC
Official Full Name: ATPase phospholipid transporting 9A (putative)provided by HGNC
Primary source: HGNC:HGNC:13540
See related: Ensembl:ENSG00000054793 MIM:609126; AllianceGenome:HGNC:13540
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: ATPIIA; NEDGBA
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, Dec 2024]
Expression: Broad expression in brain (RPKM 35.7), thyroid (RPKM 11.3) and 18 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 20q13.2

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (51596514..51768390, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (53367254..53539838, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (50213053..50384929, complement)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Circular RNA circATP9A promotes non-small cell lung cancer progression by interacting with HuR and by promoting extracellular vesicles-mediated macrophage M2 polarization.
Title: Circular RNA circATP9A promotes non-small cell lung cancer progression by interacting with HuR and by promoting extracellular vesicles-mediated macrophage M2 polarization.
The phospholipid flippase ATP9A enhances macropinocytosis to promote nutrient starvation tolerance in hepatocellular carcinoma.
Title: The phospholipid flippase ATP9A enhances macropinocytosis to promote nutrient starvation tolerance in hepatocellular carcinoma.
Biallelic truncating variants in ATP9A cause a novel neurodevelopmental disorder involving postnatal microcephaly and failure to thrive.
Title: Biallelic truncating variants in ATP9A cause a novel neurodevelopmental disorder involving postnatal microcephaly and failure to thrive.
Structural basis of the P4B ATPase lipid flippase activity.
Title: Structural basis of the P4B ATPase lipid flippase activity.
Effects of ATP9A on Extracellular Vesicle Release and Exosomal Lipid Composition.
Title: Effects of ATP9A on Extracellular Vesicle Release and Exosomal Lipid Composition.
Pharmacological blocking of exosome release in ATP9A knockdown cells did significantly reduce the total number of Extracellular vesicles . Our data support a role for ATP9A in the regulation of exosome release from human cells.
Title: The P4-ATPase ATP9A is a novel determinant of exosome release.
an evolutionary conserved MON2:DOPEY2:ATP9A complex is required for SNX3 retromer mediation of Wntless sorting and Wnt secretion
Title: SNX3-retromer requires an evolutionary conserved MON2:DOPEY2:ATP9A complex to mediate Wntless sorting and Wnt secretion.
the predominant P4 ATPases in pure pancreatic beta cells and human and rat pancreatic islets were ATP8B1, ATP8B2, and ATP9A. ATP8B1 and CDC50A were highly concentrated in ISG
Title: Characterization of P4 ATPase Phospholipid Translocases (Flippases) in Human and Rat Pancreatic Beta Cells: THEIR GENE SILENCING INHIBITS INSULIN SECRETION.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neurodevelopmental disorder with poor growth and behavioral abnormalities MedGen: C5830273 OMIM: 620242 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

G20606 (e-PCR)
- UniSTS:59932

A005Y41 (e-PCR)
- UniSTS:59933

D20S620 (e-PCR)
- UniSTS:81464

SHGC-83700 (e-PCR)
- UniSTS:104259

RH48521 (e-PCR)
- UniSTS:50500

D20S457 (e-PCR)
- UniSTS:27229

AL032541 (e-PCR)
- UniSTS:93287

A008B25 (e-PCR)
- UniSTS:10606

RH12445 (e-PCR)
- UniSTS:5493

A001W29 (e-PCR)
- UniSTS:43898

G19718 (e-PCR)
- UniSTS:43899

RH45440 (e-PCR)
- UniSTS:60541

A009A38 (e-PCR)
- UniSTS:64895

D20S579E (e-PCR)
- UniSTS:51180

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATPase-coupled intramembrane lipid transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables magnesium ion binding	IEA Inferred from Electronic Annotation more info
enables protease binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in endocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of exosomal secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron projection morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in phospholipid translocation	IBA Inferred from Biological aspect of Ancestor more info
involved_in phospholipid translocation	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of endocytic recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of retrograde transport, endosome to Golgi	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in trans-Golgi network	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: probable phospholipid-transporting ATPase IIA

Names: ATPase type IV, phospholipid-transporting (P-type),(putative); ATPase, class II, type 9A; phospholipid-transporting ATPase IIA

NP_006036.1

EC 7.6.2.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_006045.3 → NP_006036.1 probable phospholipid-transporting ATPase IIA

See identical proteins and their annotated locations for NP_006036.1

Status: VALIDATED

Source sequence(s)

AK299064, AL035684, BC110592, BF089115, HY147052

Consensus CDS

CCDS33489.1

UniProtKB/Swiss-Prot

E1P5Y3, E1P5Y4, O75110, Q5TFW5, Q5TFW6, Q5TFW9, Q6ZMF3, Q9NQK6, Q9NQK7

UniProtKB/TrEMBL

B4DR18

Related

ENSP00000342481.5, ENST00000338821.6

Conserved Domains (2) summary

cd07541
Location:55 → 967

P-type_ATPase_APLT_Neo1-like; Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Neo1p and human putative APLT, ATP9B

pfam13246
Location:464 → 571

Cation_ATPase; Cation transport ATPase (P-type)