ATP8B2
Basic information
Region (hg38): 1:154325525-154351304
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 38 | 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) | ||
1-154330822-G-A | not specified | Uncertain significance (May 27, 2022) | ||
1-154330869-C-T | not specified | Uncertain significance (Apr 21, 2022) | ||
1-154331087-A-G | not specified | Uncertain significance (Sep 06, 2022) | ||
1-154331144-T-C | not specified | Uncertain significance (Jan 04, 2024) | ||
1-154331978-A-G | not specified | Uncertain significance (Jul 12, 2023) | ||
1-154332637-C-T | not specified | Uncertain significance (Dec 19, 2023) | ||
1-154332638-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
1-154332677-G-C | not specified | Uncertain significance (Jun 22, 2024) | ||
1-154334140-T-A | not specified | Uncertain significance (Apr 19, 2024) | ||
1-154334211-C-T | not specified | Uncertain significance (Jul 12, 2023) | ||
1-154334217-T-C | not specified | Uncertain significance (May 18, 2023) | ||
1-154334590-G-C | not specified | Uncertain significance (Mar 20, 2024) | ||
1-154337423-C-T | not specified | Uncertain significance (Aug 02, 2021) | ||
1-154337442-C-G | not specified | Uncertain significance (Mar 25, 2024) | ||
1-154337442-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
1-154337534-C-T | not specified | Uncertain significance (Jun 27, 2022) | ||
1-154340911-C-A | not specified | Uncertain significance (Dec 19, 2022) | ||
1-154340952-C-T | not specified | Uncertain significance (Sep 12, 2023) | ||
1-154340959-C-T | Benign (Dec 24, 2018) | |||
1-154340980-G-C | not specified | Uncertain significance (Sep 01, 2021) | ||
1-154342874-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
1-154342958-G-A | not specified | Uncertain significance (Jul 08, 2022) | ||
1-154343293-C-G | not specified | Uncertain significance (Jun 11, 2021) | ||
1-154343547-C-T | Benign (Dec 24, 2018) |
GnomAD
Source:
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:
- 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