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.

not_specified (63 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000022735.4. 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					1 clinvar	1
missense			62 clinvar	1 clinvar		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	1	1

Loading clinvar variants...

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