ABCA9

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

Basic information

Region (hg38): 17:68974487-69060949

Links

ENSG00000154258 ∙ NCBI:10350 ∙ OMIM:612507 ∙ HGNC:39 ∙ Uniprot:Q8IUA7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCA9 gene.

• Inborn genetic diseases (75 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCA9 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				4		4
missense			69	6		75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	69	10	0

Variants in ABCA9

This is a list of pathogenic ClinVar variants found in the ABCA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-68975945-C-A		not specified	Uncertain significance (Jan 29, 2024)
17-68975964-T-C		not specified	Uncertain significance (Aug 02, 2022)
17-68976181-C-T		not specified	Likely benign (Dec 28, 2022)
17-68982582-G-T		not specified	Uncertain significance (Feb 12, 2024)
17-68982597-C-T		not specified	Uncertain significance (Apr 12, 2023)
17-68982617-C-T			Likely benign (Oct 01, 2022)
17-68983761-G-C		not specified	Uncertain significance (Nov 22, 2023)
17-68983765-C-A		not specified	Uncertain significance (Dec 07, 2021)
17-68983797-G-T		not specified	Uncertain significance (Oct 12, 2021)
17-68983820-C-G		not specified	Uncertain significance (Dec 20, 2021)
17-68984081-C-G		not specified	Uncertain significance (Mar 30, 2022)
17-68984086-C-T		not specified	Uncertain significance (Nov 30, 2022)
17-68984122-G-A		not specified	Uncertain significance (Dec 09, 2023)
17-68984165-G-A		not specified	Uncertain significance (Mar 01, 2023)
17-68984891-T-G		not specified	Uncertain significance (Mar 29, 2022)
17-68985093-T-C		not specified	Uncertain significance (Oct 27, 2021)
17-68986201-C-T		not specified	Uncertain significance (May 05, 2023)
17-68989047-T-C		not specified	Uncertain significance (Mar 16, 2023)
17-68989915-C-T		not specified	Uncertain significance (Oct 10, 2023)
17-68989921-T-C		not specified	Uncertain significance (Aug 12, 2021)
17-68990847-T-C		not specified	Uncertain significance (May 09, 2023)
17-68990852-C-T			Likely benign (Apr 01, 2023)
17-68990854-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-68992208-C-T		not specified	Uncertain significance (Nov 10, 2022)
17-68992226-C-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCA9	protein_coding	protein_coding	ENST00000340001	38	86577

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.49e-48	0.00000627	124860	1	887	125748	0.00354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.751	766	827	0.926	0.0000410	10638
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00446	0.00445
Ashkenazi Jewish	0.0164	0.0164
East Asian	0.00184	0.00180
Finnish	0.00214	0.00213
European (Non-Finnish)	0.00402	0.00393
Middle Eastern	0.00184	0.00180
South Asian	0.00216	0.00209
Other	0.00464	0.00441

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in monocyte differentiation and lipid homeostasis. {ECO:0000269|PubMed:12150964}.
• Pathway: ABC transporters - Homo sapiens (human);ABC transporters in lipid homeostasis;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Intolerance Scores

• loftool: 0.149
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.0719
• hipred: N
• hipred_score: 0.181
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.172

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abca9

Gene ontology

• Biological process: lipid transport;transmembrane transport
• Cellular component: integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: lipid transporter activity;ATP binding;ATPase activity, coupled to transmembrane movement of substances