ATP8B2

ATPase phospholipid transporting 8B2, the group of ATPase phospholipid transporting

Basic information

Region (hg38): 1:154325525-154351304

Links

ENSG00000143515

∙ NCBI:57198 ∙ OMIM:605867 ∙ HGNC:13534 ∙ Uniprot:P98198 ∙ 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 ATP8B2 gene.

not_specified (90 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP8B2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001370597.1. 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				2 clinvar	2 clinvar	4
missense			87 clinvar			87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	87	2	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP8B2	protein_coding	protein_coding	ENST00000368489	28	25755

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00563	0.994	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.87	512	730	0.701	0.0000440	8079
Missense in Polyphen		228	346.09	0.65878		3853
Synonymous	1.09	267	291	0.919	0.0000176	2382
Loss of Function	5.35	17	62.7	0.271	0.00000320	688

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000685	0.000684
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000326	0.000326

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 (Probable). {ECO:0000305}.;
Pathway: Mesodermal Commitment Pathway;Ion channel transport;Transport of small molecules;Phosphatidylinositol phosphate metabolism;Glycerophospholipid metabolism;Vitamin A (retinol) metabolism;Ion transport by P-type ATPases (Consensus)

Intolerance Scores

loftool: 0.0967
rvis_EVS: -1.66
rvis_percentile_EVS: 2.75

Haploinsufficiency Scores

pHI: 0.366
hipred: Y
hipred_score: 0.639
ghis: 0.587

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.384

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Atp8b2
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); skeleton phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype;

Gene ontology

Biological process: Golgi organization;ion transmembrane transport;phospholipid translocation
Cellular component: endoplasmic reticulum membrane;Golgi apparatus;plasma membrane;integral component of membrane
Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;ATP binding