ACBD3

acyl-CoA binding domain containing 3, the group of A-kinase anchoring proteins

Basic information

Region (hg38): 1:226144679-226186741

Previous symbols: [ "GOLPH1", "GOCAP1" ]

Links

ENSG00000182827 ∙ NCBI:64746 ∙ OMIM:606809 ∙ HGNC:15453 ∙ Uniprot:Q9H3P7 ∙ 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 ACBD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACBD3 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			41	1		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	1	1

Variants in ACBD3

This is a list of pathogenic ClinVar variants found in the ACBD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-226146650-C-T		not specified	Uncertain significance (Jan 17, 2025)
1-226146753-C-G		not specified	Uncertain significance (Oct 06, 2023)
1-226146795-T-C		not specified	Uncertain significance (Oct 08, 2024)
1-226146807-C-T		not specified	Uncertain significance (Sep 01, 2024)
1-226152345-C-G		not specified	Uncertain significance (Aug 12, 2021)
1-226152347-C-T		not specified	Uncertain significance (Nov 20, 2023)
1-226152377-C-T		not specified	Uncertain significance (Sep 11, 2024)
1-226152380-T-C		not specified	Uncertain significance (May 30, 2024)
1-226152385-G-T		not specified	Uncertain significance (Mar 21, 2024)
1-226152392-T-C		not specified	Uncertain significance (May 09, 2023)
1-226152398-A-G		not specified	Uncertain significance (Aug 05, 2024)
1-226152431-T-C		not specified	Uncertain significance (May 20, 2024)
1-226152464-G-T		not specified	Uncertain significance (Jul 06, 2021)
1-226152505-A-G		not specified	Uncertain significance (Feb 06, 2025)
1-226152530-C-T		not specified	Uncertain significance (Jun 04, 2024)
1-226152574-T-C		not specified	Uncertain significance (Oct 12, 2021)
1-226152578-G-T		not specified	Uncertain significance (Mar 15, 2024)
1-226154673-T-C		not specified	Uncertain significance (Jan 03, 2024)
1-226154714-G-T		not specified	Uncertain significance (Nov 30, 2022)
1-226154721-T-C		not specified	Uncertain significance (Aug 28, 2024)
1-226154737-C-T		not specified	Uncertain significance (Nov 10, 2024)
1-226154761-T-C		not specified	Likely benign (Nov 15, 2024)
1-226154811-T-C		not specified	Uncertain significance (Jun 01, 2023)
1-226159245-T-C		not specified	Uncertain significance (Feb 12, 2024)
1-226159351-T-C		not specified	Uncertain significance (Apr 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACBD3	protein_coding	protein_coding	ENST00000366812	8	42052

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0107	0.989	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	184	268	0.687	0.0000145	3391
Missense in Polyphen		37	74.289	0.49806		902
Synonymous	0.465	96	102	0.941	0.00000542	1010
Loss of Function	3.46	9	29.1	0.309	0.00000173	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000727	0.0000703
Middle Eastern	0.000110	0.000109
South Asian	0.0000664	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the maintenance of Golgi structure by interacting with giantin, affecting protein transport between the endoplasmic reticulum and Golgi (PubMed:11590181). Involved in hormone-induced steroid biosynthesis in testicular Leydig cells (By similarity). Recruits PI4KB to the Golgi apparatus membrane; enhances the enzyme activity of PI4KB activity via its membrane recruitment thereby increasing the local concentration of the substrate in the vicinity of the kinase (PubMed:27009356). {ECO:0000250|UniProtKB:Q8BMP6, ECO:0000269|PubMed:11590181, ECO:0000269|PubMed:27009356}.
• Pathway: Benzodiazepine Pathway, Pharmacodynamics;Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.582
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.300
• hipred: Y
• hipred_score: 0.602
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.664

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acbd3
• Phenotype: vision/eye phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: steroid biosynthetic process
• Cellular component: Golgi membrane;mitochondrion;Golgi apparatus;membrane
• Molecular function: fatty-acyl-CoA binding;protein binding;protein kinase A regulatory subunit binding