ACBD5

acyl-CoA binding domain containing 5

Basic information

Region (hg38): 10:27168134-27243046

Links

ENSG00000107897 ∙ NCBI:91452 ∙ OMIM:616618 ∙ HGNC:23338 ∙ Uniprot:Q5T8D3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinal dystrophy with leukodystrophy (Strong), mode of inheritance: AR
• retinal dystrophy with leukodystrophy (Moderate), mode of inheritance: AR
• retinal dystrophy with leukodystrophy (Definitive), mode of inheritance: AR
• acyl-CoA binding domain containing protein 5 deficiency (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinal dystrophy with leukodystrophy	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	Biochemical; Craniofacial; Neurologic; Ophthalmologic	23105016; 27799409

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACBD5 gene.

• not provided (375 variants)
• Thrombocytopenia (46 variants)
• Inborn genetic diseases (42 variants)
• not specified (9 variants)
• Retinal dystrophy with leukodystrophy (7 variants)
• MASTL-related condition (4 variants)
• Scimitar anomaly, multiple cardiac malformations, and craniofacial and central nervous system abnormalities (1 variants)
• Autosomal dominant thrombocytopenia (1 variants)
• Thrombocytopenia 2 (1 variants)
• Cone-rod dystrophy (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACBD5 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			3	54	8	65
missense			141	4	4	149
nonsense	4	2				6
start loss						0
frameshift	2	1				3
inframe indel			6			6
splice donor/acceptor (+/-2bp)		5	2			7
splice region			7	11	2	20
non coding	1		40	48	97	186
Total	7	8	192	106	109

Highest pathogenic variant AF is 0.0000394

Variants in ACBD5

This is a list of pathogenic ClinVar variants found in the ACBD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-27169639-A-C			Benign (Jun 19, 2021)
10-27169750-C-T			Benign (Jun 19, 2021)
10-27169929-T-C		Thrombocytopenia	Benign (Jan 12, 2018)
10-27169937-C-T		Thrombocytopenia	Benign (Jan 12, 2018)
10-27169955-A-G		Thrombocytopenia	Uncertain significance (Jan 13, 2018)
10-27169969-C-A		not specified • Thrombocytopenia	Benign (Jan 13, 2018)
10-27169975-T-A		Thrombocytopenia • MASTL-related disorder	Benign/Likely benign (Jan 02, 2024)
10-27169997-G-A		MASTL-related disorder	Likely benign (Feb 24, 2020)
10-27170004-G-A		Thrombocytopenia • MASTL-related disorder	Benign/Likely benign (Apr 16, 2019)
10-27170026-A-C		not specified	Uncertain significance (Feb 28, 2024)
10-27170029-C-T		not specified	Uncertain significance (Aug 16, 2021)
10-27170077-A-G		not specified	Uncertain significance (Feb 10, 2022)
10-27170106-C-T		Thrombocytopenia	Benign (Jan 12, 2018)
10-27170145-G-C		MASTL-related disorder	Likely benign (Sep 22, 2022)
10-27170148-G-T		not specified	Uncertain significance (Jun 27, 2023)
10-27170169-C-T		Thrombocytopenia	Likely benign (Jan 13, 2018)
10-27170191-T-C			Uncertain significance (Jan 19, 2017)
10-27170251-G-C		MASTL-related disorder	Uncertain significance (Nov 09, 2022)
10-27170314-C-A		Thrombocytopenia • MASTL-related disorder	Benign/Likely benign (Jul 24, 2023)
10-27170335-T-A		not specified	Uncertain significance (Oct 06, 2021)
10-27170365-A-G		not specified	Uncertain significance (Feb 14, 2023)
10-27170367-C-A		Thrombocytopenia	Uncertain significance (Jan 12, 2018)
10-27170373-G-A		MASTL-related disorder	Uncertain significance (Jan 02, 2023)
10-27170374-A-G		Thrombocytopenia	Benign (Jan 13, 2018)
10-27170382-A-G		MASTL-related disorder	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACBD5	protein_coding	protein_coding	ENST00000396271	13	46914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00615	0.994	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.873	246	288	0.855	0.0000146	3491
Missense in Polyphen		67	95.78	0.69952		1191
Synonymous	-0.464	108	102	1.06	0.00000570	937
Loss of Function	3.61	10	32.0	0.312	0.00000154	367

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000202	0.000202
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000212	0.000211
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acyl-CoA binding protein which acts as the peroxisome receptor for pexophagy but is dispensable for aggrephagy and nonselective autophagy. Binds medium- and long-chain acyl-CoA esters. {ECO:0000269|PubMed:24535825}.
• Pathway: Metabolism of lipids;Peroxisomal lipid metabolism;Metabolism;Fatty acid metabolism (Consensus)

Recessive Scores

• pRec: 0.0700

Intolerance Scores

• loftool: 0.302
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.422
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.418

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acbd5
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: fatty acid catabolic process;macroautophagy;autophagy of peroxisome;aggrephagy
• Cellular component: nucleus;nucleoplasm;peroxisome;peroxisomal membrane;membrane;integral component of membrane
• Molecular function: fatty-acyl-CoA binding;molecular_function;lipid binding