ATP9B

ATPase phospholipid transporting 9B (putative), the group of ATPase phospholipid transporting

Basic information

Region (hg38): 18:79069284-79378287

Links

ENSG00000166377 ∙ NCBI:374868 ∙ OMIM:614446 ∙ HGNC:13541 ∙ Uniprot:O43861 ∙ 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 ATP9B gene.

• Inborn genetic diseases (58 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP9B 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				3	3	6
missense			56	4	1	61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	56	7	4

Variants in ATP9B

This is a list of pathogenic ClinVar variants found in the ATP9B region.

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

Position	Type	Phenotype	Significance	ClinVar
18-79069417-G-T		not specified	Uncertain significance (Jan 22, 2024)
18-79069424-T-G		not specified	Uncertain significance (Jun 29, 2023)
18-79069427-C-T		not specified	Uncertain significance (Jul 15, 2021)
18-79069436-C-T		not specified	Uncertain significance (Oct 02, 2023)
18-79069441-C-T		not specified	Uncertain significance (Dec 15, 2023)
18-79069450-G-C		not specified	Uncertain significance (Aug 02, 2022)
18-79069458-C-T			Likely benign (Mar 01, 2022)
18-79069475-G-T		not specified	Uncertain significance (Jan 18, 2022)
18-79069481-C-T		not specified	Uncertain significance (Dec 05, 2023)
18-79069490-G-T		not specified	Uncertain significance (Jul 05, 2023)
18-79069519-C-T		not specified	Uncertain significance (Jun 17, 2022)
18-79096499-C-T		not specified	Uncertain significance (Jun 23, 2021)
18-79096502-A-T		not specified	Uncertain significance (Oct 12, 2022)
18-79096537-G-C		not specified	Uncertain significance (Dec 17, 2023)
18-79096549-G-A		not specified	Uncertain significance (Feb 15, 2023)
18-79096577-G-A		not specified	Uncertain significance (May 22, 2023)
18-79096627-G-A		not specified	Uncertain significance (Dec 12, 2023)
18-79110371-A-G		not specified	Likely benign (Dec 06, 2022)
18-79110408-G-A		not specified	Uncertain significance (May 31, 2023)
18-79110410-A-C		not specified	Uncertain significance (Sep 07, 2022)
18-79110411-C-T		not specified	Uncertain significance (Sep 07, 2022)
18-79110412-A-C			Benign (Jun 18, 2018)
18-79113346-G-A		not specified	Uncertain significance (May 04, 2022)
18-79126294-C-T		not specified	Uncertain significance (Sep 01, 2021)
18-79126295-G-A		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP9B	protein_coding	protein_coding	ENST00000426216	30	308999

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.18e-14	1.00	125635	0	113	125748	0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.691	634	685	0.926	0.0000417	7469
Missense in Polyphen		187	216.54	0.86359		2223
Synonymous	-0.363	281	273	1.03	0.0000185	2209
Loss of Function	3.63	34	65.7	0.517	0.00000331	746

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00181	0.00176
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.000495	0.000489
Finnish	0.000239	0.000231
European (Non-Finnish)	0.000425	0.000422
Middle Eastern	0.000495	0.000489
South Asian	0.000236	0.000229
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Ion channel transport;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.227
• rvis_EVS: -1.14
• rvis_percentile_EVS: 6.4

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.426
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.414

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp9b

Gene ontology

• Biological process: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;endocytosis;phospholipid translocation
• Cellular component: endosome;trans-Golgi network;plasma membrane;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;ATP binding