ACSM4

acyl-CoA synthetase medium chain family member 4, the group of Acyl-CoA synthetase family

Basic information

Region (hg38): 12:7304072-7328719

Links

ENSG00000215009

∙ NCBI:341392 ∙ OMIM:614360 ∙ HGNC:32016 ∙ Uniprot:P0C7M7 ∙ 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 ACSM4 gene.

not_specified (58 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSM4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001080454.2. 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			55 clinvar	2 clinvar		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSM4	protein_coding	protein_coding	ENST00000399422	13	24441

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.05e-19	0.00995	114123	317	10616	125056	0.0447

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.908	274	320	0.857	0.0000174	3765
Missense in Polyphen		104	110.26	0.94327		1302
Synonymous	1.24	100	117	0.855	0.00000656	1100
Loss of Function	0.471	30	32.9	0.911	0.00000184	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.147	0.147
Ashkenazi Jewish	0.0675	0.0672
East Asian	0.00753	0.00736
Finnish	0.0289	0.0284
European (Non-Finnish)	0.0457	0.0453
Middle Eastern	0.00753	0.00736
South Asian	0.0361	0.0357
Other	0.0539	0.0530

dbNSFP

Source: dbNSFP

Function: FUNCTION: Has medium-chain fatty acid:CoA ligase activity with broad substrate specificity (in vitro). Acts on acids from C(4) to C(11) and on the corresponding 3-hydroxy- and 2,3- or 3,4- unsaturated acids (in vitro) (By similarity). {ECO:0000250}.;
Pathway: Butanoate metabolism - Homo sapiens (human);Valproic Acid Pathway, Pharmacokinetics;Conjugation of salicylate with glycine;Conjugation of carboxylic acids;Amino Acid conjugation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;γ-linolenate biosynthesis;icosapentaenoate biosynthesis II (metazoa) (Consensus)

Intolerance Scores

loftool: 0.959
rvis_EVS: -0.46
rvis_percentile_EVS: 23.57

Haploinsufficiency Scores

pHI: 0.171
hipred: N
hipred_score: 0.144
ghis: 0.415

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0828

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Acsm4
Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; craniofacial phenotype; growth/size/body region phenotype; taste/olfaction phenotype;

Gene ontology

Biological process: fatty acid biosynthetic process;acyl-CoA metabolic process
Cellular component: mitochondrial matrix
Molecular function: acyl-CoA ligase activity;fatty-acyl-CoA synthase activity;ATP binding;fatty acid ligase activity;metal ion binding;butyrate-CoA ligase activity