ABCA6

protein-coding

ATP binding cassette subfamily A member 6, the group of ATP binding cassette subfamily A|MicroRNA protein coding host genes

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 and may play a role in macrophage lipid homeostasis. [provided by RefSeq, Jul 2008]

MANE transcript

NM_080284.3

Inheritance

—

ClinVar variants

U:221B:24

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr17:69,078,702-69,141,895

External References & Databases

Ensembl (ENSG00000154262)

Transcript & Mutation Effects

hg38 • Region Span ~63.2 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 ABCA6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 225

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080284.3. 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			1 clinvar	7 clinvar		8
missense			214 clinvar	17 clinvar		231
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	221	24	0	245

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080284.3	RefSeq	NP_525023.2	38	MANE Select
ENST00000284425.7	Ensembl	ENSP00000284425.1	38	MANE Select
ENST00000590645.1	Ensembl	ENSP00000466862.1	3	Standard
ENST00000590645.2	Ensembl	ENSP00000466862.1	3	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

nucleoplasm
integral component of membrane
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000284425
Coding exons: 38
Length: 63187
Individuals with no LoFs: 125279
Homozygous LoFs: 2
Heterozygous LoFs: 467
Defined: 125748
p: 0.00187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.491	824	785	1.05	0.0000377	10601
Missense (PolyPhen)		221	219.02	1.0091		3288
Synonymous	0.584	267	279	0.956	0.0000141	2947
Loss of Function	2.55	54	78.4	0.689	0.00000357	1116

Population LoF Frequency

Population	CAF	p-value	Status
African	0.012	0.012	notable
Latino/Admixed American	0.0014	0.0012	notable
Ashkenazi Jewish	0.0058	0.0058	notable
East Asian	0.0017	0.0015	notable
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00096	0.00093	rare
South Asian	0.0012	0.0010	notable
Other	0.0016	0.0015	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.0858
RVIS EVS: 0.26
RVIS percentile EVS: 70.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.116

Gene Damage Prediction

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