ABCA5

ATP binding cassette subfamily A member 5, the group of ATP binding cassette subfamily A

Basic information

Region (hg38): 17:69244311-69327244

Links

ENSG00000154265 ∙ NCBI:23461 ∙ OMIM:612503 ∙ HGNC:35 ∙ Uniprot:Q8WWZ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ventricular tachycardia, familial (Limited), mode of inheritance: Unknown
• gingival fibromatosis-hypertrichosis syndrome (Limited), mode of inheritance: AR
• gingival fibromatosis-hypertrichosis syndrome (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypertrichosis terminalis, generalized, with or without gingival hyperplasia	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dermatologic	24831815

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABCA5 gene.

• Gingival fibromatosis-hypertrichosis syndrome (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABCA5 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				12	7	19
missense			88	12	6	106
nonsense		1				1
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region				8	1	9
non coding			1	2		3
Total	1	3	89	26	13

Highest pathogenic variant AF is 0.0000197

Variants in ABCA5

This is a list of pathogenic ClinVar variants found in the ABCA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-69247565-C-G		not specified	Uncertain significance (Jan 24, 2023)
17-69247565-C-T		not specified	Uncertain significance (Jun 28, 2022)
17-69248300-T-C		not specified	Uncertain significance (Nov 10, 2022)
17-69248306-A-T		not specified	Uncertain significance (Jan 03, 2024)
17-69249902-T-C			Likely benign (Dec 31, 2019)
17-69249910-T-C		not specified	Uncertain significance (May 17, 2023)
17-69250482-G-A		not specified	Uncertain significance (Oct 25, 2023)
17-69250494-G-A		not specified	Uncertain significance (Sep 27, 2022)
17-69250524-G-A		not specified	Uncertain significance (Mar 16, 2022)
17-69250568-A-C		not specified	Uncertain significance (Aug 30, 2022)
17-69250568-A-G		not specified	Uncertain significance (Mar 07, 2023)
17-69250586-A-G		not specified	Uncertain significance (Jan 24, 2024)
17-69251740-C-T			Likely benign (Nov 17, 2017)
17-69251752-C-G		not specified	Uncertain significance (Jul 20, 2022)
17-69251753-T-C		not specified	Uncertain significance (Feb 28, 2024)
17-69251761-C-T		ABCA5-related disorder	Likely benign (Jun 25, 2019)
17-69251850-C-A		not specified	Uncertain significance (Dec 27, 2023)
17-69253570-C-T		ABCA5-related disorder	Likely benign (Mar 06, 2024)
17-69253607-T-C		not specified	Uncertain significance (Oct 27, 2022)
17-69253649-T-C		not specified	Uncertain significance (May 26, 2022)
17-69253656-A-C		ABCA5-related disorder	Likely benign (Aug 22, 2019)
17-69253793-C-G		Gingival fibromatosis-hypertrichosis syndrome • Inborn genetic diseases	Pathogenic (Oct 26, 2012)
17-69253799-G-A		Gingival fibromatosis-hypertrichosis syndrome	Likely pathogenic (Mar 29, 2024)
17-69253856-G-A		not specified	Uncertain significance (Jul 05, 2023)
17-69254325-C-G		not specified	Uncertain significance (Feb 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABCA5	protein_coding	protein_coding	ENST00000392676	38	82934

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.78e-27	0.932	125515	2	230	125747	0.000923

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.374	748	777	0.962	0.0000369	10765
Missense in Polyphen		248	270.45	0.91698		3791
Synonymous	-0.200	259	255	1.02	0.0000121	2972
Loss of Function	2.78	55	82.2	0.669	0.00000406	1162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00352	0.00343
Ashkenazi Jewish	0.00	0.00
East Asian	0.00135	0.00131
Finnish	0.000469	0.000462
European (Non-Finnish)	0.000730	0.000695
Middle Eastern	0.00135	0.00131
South Asian	0.00114	0.00108
Other	0.000559	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the processing of autolysosomes. {ECO:0000250}.
• Pathway: ABC transporters - Homo sapiens (human);ABC transporters in lipid homeostasis;Transport of small molecules;ABC-family proteins mediated transport (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.0437
• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.96

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.414
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0698

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abca5
• Phenotype: vision/eye phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); endocrine/exocrine gland phenotype; muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: lipid transport;negative regulation of macrophage derived foam cell differentiation;cholesterol efflux;high-density lipoprotein particle remodeling;reverse cholesterol transport;transmembrane transport
• Cellular component: Golgi membrane;lysosome;lysosomal membrane;late endosome;Golgi apparatus;integral component of membrane;late endosome membrane;intracellular membrane-bounded organelle
• Molecular function: lipid transporter activity;ATP binding;ATPase activity, coupled to transmembrane movement of substances