ATP11C

ATPase phospholipid transporting 11C, the group of ATPase phospholipid transporting|MicroRNA protein coding host genes

Basic information

Region (hg38): X:139726345-139945276

Links

ENSG00000101974 ∙ NCBI:286410 ∙ OMIM:300516 ∙ HGNC:13554 ∙ Uniprot:Q8NB49 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• X-linked congenital hemolytic anemia (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hemolytic anemia, congenital, X-linked	XL	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	Hematologic	26944472

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP11C gene.

• Inborn genetic diseases (28 variants)
• X-linked congenital hemolytic anemia (20 variants)
• not provided (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP11C 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				5	2	7
missense		1	42		1	44
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1	1	3
non coding						0
Total	0	1	44	5	3

Variants in ATP11C

This is a list of pathogenic ClinVar variants found in the ATP11C region.

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

Position	Type	Phenotype	Significance	ClinVar
X-139731687-T-C			Likely benign (Dec 01, 2022)
X-139737987-G-T		not specified	Uncertain significance (Feb 15, 2023)
X-139738013-A-C		not specified	Uncertain significance (Apr 26, 2023)
X-139738029-G-C		X-linked congenital hemolytic anemia	Uncertain significance (Nov 16, 2022)
X-139738051-C-G		not specified	Uncertain significance (Apr 11, 2023)
X-139738068-G-A		not specified	Uncertain significance (Mar 01, 2024)
X-139741027-T-C		not specified	Uncertain significance (May 18, 2023)
X-139741062-T-C		X-linked congenital hemolytic anemia	Uncertain significance (Aug 18, 2022)
X-139741069-G-A		X-linked congenital hemolytic anemia	Uncertain significance (Mar 06, 2023)
X-139741078-C-T		not specified	Uncertain significance (Dec 06, 2022)
X-139743597-T-C		X-linked congenital hemolytic anemia	Uncertain significance (May 24, 2023)
X-139745763-A-C		not specified	Uncertain significance (Nov 14, 2023)
X-139745781-C-T		ATP11C-related disorder	Benign (Dec 31, 2019)
X-139745814-A-G		not specified	Uncertain significance (Sep 06, 2022)
X-139745815-T-C			Likely benign (Jun 01, 2022)
X-139745823-G-A		not specified	Uncertain significance (Jan 04, 2022)
X-139750151-G-A		X-linked congenital hemolytic anemia	Uncertain significance (Dec 18, 2021)
X-139757855-T-C		not specified	Uncertain significance (Jan 03, 2024)
X-139762058-G-A		X-linked congenital hemolytic anemia	Uncertain significance (Oct 05, 2021)
X-139762073-C-G		not specified	Uncertain significance (Jan 27, 2022)
X-139763425-A-T			Benign (Dec 14, 2017)
X-139768298-C-A		X-linked congenital hemolytic anemia	Uncertain significance (Jun 08, 2021)
X-139768417-T-C		not specified	Uncertain significance (Jun 29, 2023)
X-139774697-A-C		not specified	Uncertain significance (Jul 05, 2023)
X-139774747-A-C		X-linked congenital hemolytic anemia • not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP11C	protein_coding	protein_coding	ENST00000327569	29	218931

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000296	125726	5	9	125740	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	275	385	0.715	0.0000279	7419
Missense in Polyphen		111	185.43	0.5986		3578
Synonymous	1.30	117	136	0.859	0.00000979	2125
Loss of Function	5.55	5	45.3	0.110	0.00000354	839

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000229	0.000197
Ashkenazi Jewish	0.000140	0.0000992
East Asian	0.0000747	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000506	0.0000352
Middle Eastern	0.0000747	0.0000544
South Asian	0.000166	0.0000980
Other	0.000235	0.000163

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. Required for B cell differentiation past the pro-B cell stage. Seems to mediate phosphatidylserine (PS) flipping in pro-B cells. May be involved in the transport of cholestatic bile acids (By similarity). {ECO:0000250}.
• Pathway: Ion channel transport;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.214
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.06

Haploinsufficiency Scores

• pHI: 0.480
• hipred: Y
• hipred_score: 0.728
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.110

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp11c
• Phenotype: homeostasis/metabolism phenotype; neoplasm; immune system phenotype; hematopoietic system phenotype; normal phenotype

Gene ontology

• Biological process: pre-B cell differentiation;ion transmembrane transport;phospholipid translocation;positive regulation of B cell differentiation
• Cellular component: lysosomal membrane;endoplasmic reticulum;endoplasmic reticulum membrane;trans-Golgi network;plasma membrane;integral component of membrane;recycling endosome
• Molecular function: magnesium ion binding;phospholipid-translocating ATPase activity;protein binding;ATP binding