ABCA10

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

Basic information

Region (hg38): 17:69147214-69244846

Links

ENSG00000154263 ∙ NCBI:10349 ∙ OMIM:612508 ∙ HGNC:30 ∙ Uniprot:Q8WWZ4 ∙ 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 ABCA10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCA10 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				1		1
missense			85	4		89
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	85	5	2

Variants in ABCA10

This is a list of pathogenic ClinVar variants found in the ABCA10 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-69148856-A-G		not specified	Uncertain significance (Jun 28, 2024)
17-69148885-A-C		not specified	Uncertain significance (Dec 21, 2023)
17-69148925-C-A		not specified	Uncertain significance (Jul 05, 2024)
17-69149049-TGA-T		not specified	Benign (Mar 29, 2016)
17-69149988-C-A		not specified	Uncertain significance (Jan 30, 2024)
17-69150032-C-A		not specified	Uncertain significance (Feb 15, 2023)
17-69150063-T-A		not specified	Uncertain significance (Jan 30, 2024)
17-69152059-C-T		not specified	Uncertain significance (Feb 06, 2024)
17-69152064-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-69152071-G-A		not specified	Uncertain significance (Jun 17, 2022)
17-69152100-A-C		not specified	Uncertain significance (Aug 12, 2021)
17-69152110-G-C		not specified	Uncertain significance (Sep 11, 2024)
17-69152182-A-G		not specified	Uncertain significance (Jan 18, 2023)
17-69152380-A-G		not specified	Uncertain significance (Jun 22, 2023)
17-69152384-T-G		not specified	Uncertain significance (Nov 24, 2024)
17-69152462-C-A		not specified	Likely benign (Sep 22, 2022)
17-69152462-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-69153324-C-T		not specified	Uncertain significance (Sep 17, 2021)
17-69153344-G-A		not specified	Uncertain significance (May 14, 2024)
17-69153350-T-C		not specified	Uncertain significance (Jul 31, 2024)
17-69153365-G-A		not specified	Uncertain significance (Dec 09, 2024)
17-69153399-G-C		not specified	Uncertain significance (Aug 10, 2021)
17-69153509-C-G		not specified	Uncertain significance (Dec 14, 2021)
17-69153525-G-A			Likely benign (Mar 01, 2023)
17-69153876-G-A		not specified	Uncertain significance (Nov 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCA10	protein_coding	protein_coding	ENST00000269081	37	97633

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.66e-34	0.0141	100626	2159	22963	125748	0.105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0555	772	768	1.01	0.0000369	10169
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	1.42	0.809
Ashkenazi Jewish	0.139	0.0692
East Asian	0.297	0.158
Finnish	0.173	0.0865
European (Non-Finnish)	0.106	0.0535
Middle Eastern	0.297	0.158
South Asian	0.144	0.0744
Other	0.186	0.0908

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transporter which may play a role in macrophage lipid homeostasis.
• Pathway: ABC transporters - Homo sapiens (human);ABC transporters in lipid homeostasis;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Intolerance Scores

• loftool: 0.131
• rvis_EVS: 1.04
• rvis_percentile_EVS: 91.15

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.112
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0399

Gene Damage Prediction

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

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