ABCA9

protein-coding

ATP binding cassette subfamily A member 9, the group of ATP binding cassette subfamily A

Gene summary

This gene is a member of the superfamily of ATP-binding cassette (ABC) transporters and the encoded protein contains two transmembrane domains and two nucleotide binding folds. 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 gene is a member of the ABC1 subfamily and is clustered with four other ABC1 family members on chromosome 17q24. Transcriptional expression of this gene is induced during monocyte differentiation into macrophages and is suppressed by cholesterol import. [provided by RefSeq, Jul 2008]

MANE transcript

NM_080283.4

Inheritance

—

ClinVar variants

U:215B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr17:68,974,488-69,060,949

External References & Databases

Ensembl (ENSG00000154258)

Transcript & Mutation Effects

hg38 • Region Span ~86.5 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 ABCA9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 219

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080283.4. 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			208 clinvar	13 clinvar		221
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	215	20	0	235

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080283.4	RefSeq	NP_525022.2	38	MANE Select
ENST00000340001.9	Ensembl	ENSP00000342216.3	38	MANE Select
ENST00000453985.6	Ensembl	ENSP00000394264.2	37	Standard
ENST00000453985.7	Ensembl	ENSP00000394264.2	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: ENST00000340001
Coding exons: 38
Length: 86577
Individuals with no LoFs: 124860
Homozygous LoFs: 1
Heterozygous LoFs: 887
Defined: 125748
p: 0.00354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.751	766	827	0.926	0.0000410	10638
Missense (PolyPhen)		163	200.88	0.81144		2826
Synonymous	0.484	299	310	0.965	0.0000163	3055
Loss of Function	0.988	78	88.0	0.886	0.00000457	1086

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0014	notable
Latino/Admixed American	0.0030	0.0025	notable
Ashkenazi Jewish	0.016	0.016	notable
East Asian	0.0018	0.0018	notable
Finnish	0.0021	0.0021	notable
European (Non-Finnish)	0.0040	0.0039	notable
South Asian	0.0022	0.0021	notable
Other	0.0046	0.0044	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in monocyte differentiation and lipid homeostasis. {ECO:0000269|PubMed:12150964}.;

Intolerance Scores

LoFtool: 0.149
RVIS EVS: 0
RVIS percentile EVS: 53.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.172

Gene Damage Prediction

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