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
gingival fibromatosis-hypertrichosis syndrome (Limited), mode of inheritance: AR

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.

not_specified (188 variants)
not_provided (35 variants)
ABCA5-related_disorder (20 variants)
Gingival_fibromatosis-hypertrichosis_syndrome (7 variants)
See_cases (2 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. These statistics are base on transcript: NM_000172232.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				14 clinvar	5 clinvar	19
missense		1 clinvar	182 clinvar	17 clinvar	4 clinvar	204
nonsense		1 clinvar				1
start loss						0
frameshift		2 clinvar				2
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	1	4	182	31	9

Highest pathogenic variant AF is 0.0000987336

Loading clinvar variants...

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