ATP8B2

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

Basic information

Region (hg38): 1:154325525-154351304

Links

ENSG00000143515NCBI:57198OMIM:605867HGNC:13534Uniprot:P98198AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP8B2 gene.

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.

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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
2
clinvar
2
missense
38
clinvar
38
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 38 0 2

Variants in ATP8B2

This is a list of pathogenic ClinVar variants found in the ATP8B2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
1-154328167-C-T not specified Uncertain significance (May 11, 2022)2386986
1-154330822-G-A not specified Uncertain significance (May 27, 2022)2387377
1-154330869-C-T not specified Uncertain significance (Apr 21, 2022)2310967
1-154331087-A-G not specified Uncertain significance (Sep 06, 2022)2310720
1-154331144-T-C not specified Uncertain significance (Jan 04, 2024)3131986
1-154331978-A-G not specified Uncertain significance (Jul 12, 2023)2610954
1-154332637-C-T not specified Uncertain significance (Dec 19, 2023)3131987
1-154332638-G-A not specified Uncertain significance (Feb 28, 2024)3131988
1-154332677-G-C not specified Uncertain significance (Jun 22, 2024)3330037
1-154334140-T-A not specified Uncertain significance (Apr 19, 2024)3329991
1-154334211-C-T not specified Uncertain significance (Jul 12, 2023)2611306
1-154334217-T-C not specified Uncertain significance (May 18, 2023)2548748
1-154334590-G-C not specified Uncertain significance (Mar 20, 2024)3329981
1-154337423-C-T not specified Uncertain significance (Aug 02, 2021)3131978
1-154337442-C-G not specified Uncertain significance (Mar 25, 2024)3329931
1-154337442-C-T not specified Uncertain significance (Nov 10, 2022)2355773
1-154337534-C-T not specified Uncertain significance (Jun 27, 2022)2372670
1-154340911-C-A not specified Uncertain significance (Dec 19, 2022)2337311
1-154340952-C-T not specified Uncertain significance (Sep 12, 2023)2622681
1-154340959-C-T Benign (Dec 24, 2018)767705
1-154340980-G-C not specified Uncertain significance (Sep 01, 2021)2248490
1-154342874-G-A not specified Uncertain significance (Jun 06, 2023)2523659
1-154342958-G-A not specified Uncertain significance (Jul 08, 2022)2220030
1-154343293-C-G not specified Uncertain significance (Jun 11, 2021)2216153
1-154343547-C-T Benign (Dec 24, 2018)777936

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ATP8B2protein_codingprotein_codingENST00000368489 2825755
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.005630.9941257050431257480.000171
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.875127300.7010.00004408079
Missense in Polyphen228346.090.658783853
Synonymous1.092672910.9190.00001762382
Loss of Function5.351762.70.2710.00000320688

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006850.000684
Ashkenazi Jewish0.00009920.0000992
East Asian0.0001630.000163
Finnish0.00004620.0000462
European (Non-Finnish)0.0001230.000123
Middle Eastern0.0001630.000163
South Asian0.0001310.000131
Other0.0003260.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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