ABCA6

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

Basic information

Region (hg38): 17:69078702-69141895

Links

ENSG00000154262 ∙ NCBI:23460 ∙ OMIM:612504 ∙ HGNC:36 ∙ Uniprot:Q8N139 ∙ 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 ABCA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCA6 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				5		5
missense			90	6		96
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	90	11	0

Variants in ABCA6

This is a list of pathogenic ClinVar variants found in the ABCA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-69079037-T-C		not specified	Uncertain significance (Oct 03, 2022)
17-69079220-G-A		not specified	Uncertain significance (Dec 21, 2022)
17-69082939-G-T		not specified	Uncertain significance (Dec 07, 2021)
17-69082979-G-A		not specified	Likely benign (May 23, 2023)
17-69082980-T-A		not specified	Uncertain significance (Sep 22, 2023)
17-69083217-C-G		not specified	Uncertain significance (Mar 28, 2024)
17-69083243-G-A		not specified	Uncertain significance (Jun 07, 2023)
17-69083259-C-T			Likely benign (Jan 01, 2023)
17-69083312-C-T		not specified	Likely benign (Jan 06, 2023)
17-69084294-G-C		not specified	Uncertain significance (Jan 03, 2024)
17-69084483-A-T		not specified	Uncertain significance (Aug 02, 2021)
17-69085038-C-T		not specified	Uncertain significance (Jul 13, 2021)
17-69085046-G-T		not specified	Uncertain significance (Mar 29, 2023)
17-69085052-G-A		not specified	Likely benign (Oct 26, 2022)
17-69085124-T-C		not specified	Uncertain significance (Mar 20, 2024)
17-69085128-C-G		not specified	Uncertain significance (Jan 26, 2022)
17-69085133-G-T		not specified	Uncertain significance (Feb 16, 2023)
17-69085134-G-C		not specified	Uncertain significance (Feb 16, 2023)
17-69085151-C-A		not specified	Uncertain significance (Oct 17, 2023)
17-69085630-C-T		not specified	Uncertain significance (Aug 16, 2021)
17-69085696-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-69086644-C-A		not specified	Uncertain significance (Jun 29, 2023)
17-69086646-T-C			Likely benign (May 01, 2023)
17-69086658-C-A		not specified	Uncertain significance (Mar 23, 2022)
17-69086666-T-A		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCA6	protein_coding	protein_coding	ENST00000284425	38	63187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.11e-27	0.793	125279	2	467	125748	0.00187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.491	824	785	1.05	0.0000377	10601
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0137	0.0131
Ashkenazi Jewish	0.00579	0.00577
East Asian	0.00167	0.00152
Finnish	0.000285	0.000277
European (Non-Finnish)	0.000961	0.000932
Middle Eastern	0.00167	0.00152
South Asian	0.00124	0.00105
Other	0.00164	0.00147

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)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.0858
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.0466
• hipred: N
• hipred_score: 0.214
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abca6
• Phenotype: hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

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