ABCA10

protein-coding

ATP binding cassette subfamily A member 10, the group of ATP binding cassette subfamily A

Gene summary

The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This encoded protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This gene is clustered among 4 other ABC1 family members on 17q24, but neither the substrate nor the function of this gene is known. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001377321.1

Inheritance

—

ClinVar variants

U:201B:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr17:69,147,214-69,244,846

External References & Databases

Ensembl (ENSG00000154263)

Transcript & Mutation Effects

hg38 • Region Span ~97.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ABCA10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 205

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001377321.1. 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			2 clinvar	1 clinvar		3
missense			194 clinvar	16 clinvar		210
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar		1 clinvar	2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	201	17	1	219

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001377321.1	RefSeq	NP_001364250.1	37	MANE Select
ENST00000690296.1	Ensembl	ENSP00000509702.1	37	MANE Select
NM_080282.4	RefSeq	NP_525021.3	37	Standard
ENST00000269081.8	Ensembl	ENSP00000269081.4	37	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

ABC transporters - Homo sapiens (human)
ABC transporters in lipid homeostasis
Transport of small molecules
ABC-family proteins mediated transport

Biological Process

lipid transport
transmembrane transport

Molecular Function

lipid transporter activity
ATP binding
ATPase activity, coupled to transmembrane movement of substances

Cellular Component

integral component of membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000269081
Coding exons: 37
Length: 97633
Individuals with no LoFs: 100626
Homozygous LoFs: 2159
Heterozygous LoFs: 22963
Defined: 125748
p: 0.105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0555	772	768	1.01	0.0000369	10169
Missense (PolyPhen)		170	201.01	0.84574		2899
Synonymous	0.219	259	264	0.983	0.0000130	2794
Loss of Function	1.79	61	78.0	0.782	0.00000366	1081

Population LoF Frequency

Population	CAF	p-value	Status
African	1.0	0.43	notable
Latino/Admixed American	0.38	0.19	notable
Ashkenazi Jewish	0.14	0.069	notable
East Asian	0.30	0.16	notable
Finnish	0.17	0.087	notable
European (Non-Finnish)	0.11	0.054	notable
South Asian	0.14	0.074	notable
Other	0.19	0.091	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable transporter which may play a role in macrophage lipid homeostasis.;

Intolerance Scores

LoFtool: 0.131
RVIS EVS: 1.04
RVIS percentile EVS: 91.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0399

Gene Damage Prediction

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