ATP11C

protein-coding

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

Gene summary

Enables phosphatidylethanolamine flippase activity and phosphatidylserine flippase activity. Involved in phospholipid translocation. Located in endoplasmic reticulum and plasma membrane. Part of phospholipid-translocating ATPase complex. Implicated in X-linked congenital hemolytic anemia. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001353812.2

Inheritance

ClinVar variants

P:3U:326B:19

Top phenotype

Hemolytic anemia, congenital, X-linked

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chrX:139,726,346-139,945,276

External References & Databases

Ensembl (ENSG00000101974)

Transcript & Mutation Effects

hg38 • Region Span ~218.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

X-linked congenital hemolytic anemiaLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0060455

Submitter: Ambry Genetics

X-linked congenital hemolytic anemiaLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0060455

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Hemolytic anemia, congenital, X-linkedXL

Manifestation: Hematologic

Intervention: General

Rationale: 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

Refs: 26944472

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATP11C variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 102

not providedTotal: 54

ATP11C-related disorderTotal: 8

X-linked congenital hemolytic anemiaTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001353812.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			40 clinvar	10 clinvar	2 clinvar	52
missense		1 clinvar	219 clinvar	5 clinvar	2 clinvar	227
nonsense			24 clinvar			24
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar	41 clinvar			43
Total	1	2	326	15	4	348

Highest pathogenic variant AF is 0.0000038037495

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001353812.2	RefSeq	NP_001340741.2	29	MANE Select
ENST00000682941.1	Ensembl	ENSP00000507250.1	29	MANE Select
NM_001010986.3	RefSeq	NP_001010986.2	29	Standard
NM_001353810.2	RefSeq	NP_001340739.2	29	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ion channel transport
Transport of small molecules
Ion transport by P-type ATPases

Biological Process

pre-B cell differentiation
ion transmembrane transport
phospholipid translocation
positive regulation of B cell differentiation

Molecular Function

magnesium ion binding
phospholipid-translocating ATPase activity
protein binding
ATP binding

Cellular Component

lysosomal membrane
endoplasmic reticulum
endoplasmic reticulum membrane
trans-Golgi network
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000327569
Coding exons: 29
Length: 218931
Individuals with no LoFs: 125726
Homozygous LoFs: 5
Heterozygous LoFs: 9
Defined: 125740
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.99	275	385	0.715	0.0000279	7419
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00015	0.00012	rare
Latino/Admixed American	0.000074	0.000058	rare
Ashkenazi Jewish	0.00014	0.000099	rare
East Asian	0.000075	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000051	0.000035	rare
South Asian	0.00017	0.000098	rare
Other	0.00023	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.214
RVIS EVS: -0.31
RVIS percentile EVS: 32.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.110

Gene Damage Prediction

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