ATP8A1

ATPase phospholipid transporting 8A1, the group of ATPase phospholipid transporting

Basic information

Region (hg38): 4:42408373-42657121

Links

ENSG00000124406

∙ NCBI:10396 ∙ OMIM:609542 ∙ HGNC:13531 ∙ Uniprot:Q9Y2Q0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP8A1 gene.

not_specified (89 variants)
not_provided (1 variants)
Autism_spectrum_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP8A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006095.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			89 clinvar	1 clinvar		90
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	89	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP8A1	protein_coding	protein_coding	ENST00000381668	37	248733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.200	0.800	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.61	427	608	0.702	0.0000309	7607
Missense in Polyphen		180	292.3	0.6158		3823
Synonymous	-0.289	226	221	1.02	0.0000120	2170
Loss of Function	6.24	18	77.2	0.233	0.00000404	920

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000365
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000276	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000256	0.000255
Middle Eastern	0.000276	0.000272
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalytic component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids from the outer to the inner leaflet of various membranes and ensures the maintenance of asymmetric distribution of phospholipids. Phospholipid translocation seems also to be implicated in vesicle formation and in uptake of lipid signaling molecules. In vitro, its ATPase activity is selectively and stereospecifically stimulated by phosphatidylserine (PS). The flippase complex ATP8A1:TMEM30A seems to play a role in regulation of cell migration probably involving flippase-mediated translocation of phosphatidylethanolamine (PE) at the plasma membrane. Acts as aminophospholipid translocase at the plasma membrane in neuronal cells.;
Pathway: Peptide GPCRs;Neutrophil degranulation;Ion channel transport;Innate Immune System;Immune System;Transport of small molecules;Phosphatidylinositol phosphate metabolism;Glycerophospholipid metabolism;Vitamin A (retinol) metabolism;Ion transport by P-type ATPases (Consensus)

Recessive Scores

pRec: 0.111

Intolerance Scores

loftool: 0.204
rvis_EVS: -0.64
rvis_percentile_EVS: 16.68

Haploinsufficiency Scores

pHI: 0.799
hipred: Y
hipred_score: 0.685
ghis: 0.546

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.291

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Atp8a1
Phenotype: hematopoietic system phenotype; growth/size/body region phenotype; normal phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: learning;positive regulation of cell migration;ion transmembrane transport;neutrophil degranulation;phospholipid translocation;positive regulation of phospholipid translocation;ATP hydrolysis coupled cation transmembrane transport
Cellular component: endoplasmic reticulum;Golgi apparatus;trans-Golgi network;plasma membrane;membrane;integral component of membrane;azurophil granule membrane;specific granule membrane;chromaffin granule membrane;intracellular membrane-bounded organelle;extracellular exosome
Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;protein binding;ATP binding;cation-transporting ATPase activity