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.

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.

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						0
missense			24	2		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in ACSM4

This is a list of pathogenic ClinVar variants found in the ACSM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-7304347-C-T		not specified	Uncertain significance (Apr 07, 2022)
12-7304384-C-T		not specified	Uncertain significance (Feb 05, 2024)
12-7304395-C-T		not specified	Uncertain significance (Apr 06, 2022)
12-7304396-G-A		not specified	Likely benign (Oct 20, 2023)
12-7304426-C-T		not specified	Uncertain significance (Mar 04, 2024)
12-7304479-A-G		not specified	Uncertain significance (Jan 10, 2023)
12-7306596-T-C		not specified	Uncertain significance (Feb 02, 2024)
12-7306615-G-A		not specified	Uncertain significance (Jun 17, 2024)
12-7306695-C-T		not specified	Uncertain significance (Feb 06, 2024)
12-7306726-T-C		not specified	Uncertain significance (Nov 21, 2022)
12-7306738-G-A		not specified	Uncertain significance (Jun 18, 2021)
12-7310547-T-A		not specified	Uncertain significance (May 17, 2023)
12-7310655-T-C		not specified	Uncertain significance (Dec 16, 2022)
12-7310659-T-G		not specified	Uncertain significance (Nov 03, 2022)
12-7310680-T-A		not specified	Uncertain significance (Sep 26, 2023)
12-7310697-G-A		not specified	Uncertain significance (May 27, 2022)
12-7317183-C-T		not specified	Uncertain significance (Dec 07, 2023)
12-7317206-T-A		not specified	Uncertain significance (May 30, 2024)
12-7317208-G-T		not specified	Uncertain significance (Dec 01, 2022)
12-7317259-T-C		not specified	Uncertain significance (Dec 01, 2022)
12-7317264-T-C		not specified	Likely benign (Jan 04, 2024)
12-7317276-G-A		not specified	Uncertain significance (Nov 01, 2022)
12-7318076-C-T		not specified	Uncertain significance (Feb 03, 2022)
12-7320764-C-A		not specified	Uncertain significance (Nov 23, 2022)
12-7323469-A-G		not specified	Uncertain significance (Apr 04, 2024)

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