ACSM5

acyl-CoA synthetase medium chain family member 5, the group of Acyl-CoA synthetase family

Basic information

Region (hg38): 16:20409534-20441336

Links

ENSG00000183549 ∙ NCBI:54988 ∙ OMIM:614361 ∙ HGNC:26060 ∙ Uniprot:Q6NUN0 ∙ 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 ACSM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSM5 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				2		2
missense			36	2	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	36	4	2

Variants in ACSM5

This is a list of pathogenic ClinVar variants found in the ACSM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20411649-C-T			Likely benign (Jun 01, 2022)
16-20418099-A-G		not specified	Uncertain significance (May 16, 2024)
16-20418116-A-G		not specified	Likely benign (Sep 26, 2023)
16-20418164-A-C		not specified	Uncertain significance (Feb 23, 2023)
16-20418194-C-T		not specified	Uncertain significance (Apr 09, 2024)
16-20418258-G-A		not specified	Uncertain significance (Nov 22, 2023)
16-20418258-G-T		not specified	Uncertain significance (Jun 22, 2021)
16-20419281-C-T		not specified	Uncertain significance (May 08, 2024)
16-20419395-A-T		not specified	Uncertain significance (Nov 09, 2023)
16-20419401-C-T		not specified	Uncertain significance (Feb 07, 2023)
16-20419434-C-T		not specified	Uncertain significance (Jun 30, 2022)
16-20421272-A-C		not specified	Uncertain significance (Dec 20, 2023)
16-20421376-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-20421394-A-G		not specified	Uncertain significance (Dec 03, 2021)
16-20421397-G-A		not specified	Uncertain significance (Jun 05, 2023)
16-20423917-C-T		not specified	Uncertain significance (Aug 12, 2021)
16-20423944-A-G		not specified	Uncertain significance (Mar 28, 2024)
16-20423993-T-C		not specified	Uncertain significance (Jan 17, 2024)
16-20424005-G-T		not specified	Uncertain significance (Jun 21, 2021)
16-20424059-T-C		not specified	Uncertain significance (Aug 01, 2023)
16-20427789-C-T		not specified	Uncertain significance (Jan 06, 2023)
16-20427806-A-G		not specified	Uncertain significance (Oct 26, 2022)
16-20427860-C-G		not specified	Uncertain significance (Oct 25, 2023)
16-20427877-G-A			Benign (Apr 10, 2018)
16-20429709-A-C		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSM5	protein_coding	protein_coding	ENST00000331849	13	31803

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.17e-18	0.00968	125376	0	372	125748	0.00148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.621	367	335	1.10	0.0000190	3732
Missense in Polyphen		118	114.93	1.0267		1312
Synonymous	-2.11	165	134	1.23	0.00000814	1161
Loss of Function	0.402	29	31.4	0.923	0.00000158	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00216	0.00215
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00109	0.00109
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000432	0.000431
Middle Eastern	0.00109	0.00109
South Asian	0.00817	0.00820
Other	0.000489	0.000489

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)

Recessive Scores

• pRec: 0.0925

Intolerance Scores

• loftool: 0.816
• rvis_EVS: 3.18
• rvis_percentile_EVS: 99.33

Haploinsufficiency Scores

• pHI: 0.0551
• hipred: N
• hipred_score: 0.199

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.176

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Acsm5

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;GTP binding;fatty acid ligase activity;metal ion binding;butyrate-CoA ligase activity