ATP9A

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

Basic information

Region (hg38): 20:51596514-51768390

Links

ENSG00000054793 ∙ NCBI:10079 ∙ OMIM:609126 ∙ HGNC:13540 ∙ Uniprot:O75110 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with poor growth and behavioral abnormalities (Strong), mode of inheritance: AR
• neurodevelopmental disorder with poor growth and behavioral abnormalities (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with poor growth and behavioral abnormalities	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	34379057; 34764295; 36604604

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP9A gene.

• Neurodevelopmental disorder with poor growth and behavioral abnormalities (2 variants)
• See cases (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP9A 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	4	7
missense			33		1	34
nonsense	1					1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)	2					2
splice region			2			2
non coding						0
Total	3	1	33	3	5

Variants in ATP9A

This is a list of pathogenic ClinVar variants found in the ATP9A region.

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

Position	Type	Phenotype	Significance	ClinVar
20-51601272-T-C		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)
20-51601329-G-A		Inborn genetic diseases	Uncertain significance (Jun 30, 2023)
20-51604848-G-A			Benign (May 15, 2018)
20-51604981-G-A		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
20-51608617-T-A			Benign (Oct 19, 2017)
20-51613751-G-A		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
20-51618736-C-T		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
20-51619001-G-A		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
20-51622078-C-T		Neurodevelopmental disorder with poor growth and behavioral abnormalities	Uncertain significance (Apr 04, 2024)
20-51622156-CCT-C		Neurodevelopmental disorder with poor growth and behavioral abnormalities	Likely pathogenic (Oct 04, 2024)
20-51625223-G-A		Inborn genetic diseases	Uncertain significance (Jun 10, 2022)
20-51625262-G-A			Uncertain significance (May 10, 2024)
20-51627647-C-T		Inborn genetic diseases	Uncertain significance (Jan 06, 2023)
20-51627655-C-T		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
20-51627668-G-A		Neurodevelopmental disorder with poor growth and behavioral abnormalities	Likely pathogenic (Oct 04, 2024)
20-51629050-G-A		Inborn genetic diseases	Uncertain significance (Dec 06, 2022)
20-51639348-C-G		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
20-51639441-T-C		Inborn genetic diseases	Uncertain significance (Apr 18, 2023)
20-51656984-T-C		Inborn genetic diseases	Uncertain significance (May 12, 2024)
20-51656992-G-A			Benign (Jul 04, 2018)
20-51657053-G-A		Inborn genetic diseases	Uncertain significance (Oct 27, 2023)
20-51657119-G-A		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
20-51657131-G-A		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
20-51657150-G-C		Inborn genetic diseases	Uncertain significance (Aug 15, 2023)
20-51671130-G-GT		Neurodevelopmental disorder with poor growth and behavioral abnormalities	Likely pathogenic (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP9A	protein_coding	protein_coding	ENST00000338821	28	172121

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000684	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.15	347	644	0.539	0.0000415	6778
Missense in Polyphen		87	187.14	0.4649		1886
Synonymous	-1.88	313	273	1.14	0.0000197	2072
Loss of Function	6.62	7	64.2	0.109	0.00000354	680

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.104
• rvis_EVS: -1.64
• rvis_percentile_EVS: 2.8

Haploinsufficiency Scores

• pHI: 0.139
• hipred: Y
• hipred_score: 0.685
• ghis: 0.656

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.217

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp9a

Gene ontology

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