ACSM2A

acyl-CoA synthetase medium chain family member 2A, the group of Acyl-CoA synthetase family

Basic information

Region (hg38): 16:20451461-20487669

Previous symbols: [ "ACSM2" ]

Links

ENSG00000183747 ∙ NCBI:123876 ∙ OMIM:614358 ∙ HGNC:32017 ∙ Uniprot:Q08AH3 ∙ 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 ACSM2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSM2A 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			42	2		44
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	3	0

Variants in ACSM2A

This is a list of pathogenic ClinVar variants found in the ACSM2A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20460132-A-C		not specified	Uncertain significance (Jan 03, 2024)
16-20460175-C-T		not specified	Uncertain significance (Mar 30, 2024)
16-20460186-C-G		Abnormality of neuronal migration	Benign (Oct 31, 2014)
16-20460215-A-G		not specified	Uncertain significance (Sep 22, 2022)
16-20460224-A-G		not specified	Uncertain significance (Jan 24, 2023)
16-20460236-C-A		not specified	Uncertain significance (Sep 16, 2021)
16-20460269-A-C		not specified	Uncertain significance (Feb 15, 2023)
16-20460283-A-G		not specified	Uncertain significance (Jan 24, 2023)
16-20465517-G-A		not specified	Uncertain significance (Jan 16, 2024)
16-20465518-C-T		not specified	Uncertain significance (Aug 02, 2021)
16-20465583-A-C		not specified	Uncertain significance (Feb 28, 2024)
16-20465590-G-A		not specified	Uncertain significance (Dec 02, 2024)
16-20465595-C-A		not specified	Uncertain significance (Jun 29, 2023)
16-20465616-G-A		not specified	Uncertain significance (Aug 07, 2024)
16-20465632-C-T		not specified	Uncertain significance (Jan 29, 2024)
16-20465634-G-C		not specified	Uncertain significance (Jan 06, 2023)
16-20465644-G-A		not specified	Uncertain significance (Dec 28, 2023)
16-20465653-G-A		not specified	Uncertain significance (Jul 19, 2023)
16-20465699-G-A			Likely benign (Feb 01, 2023)
16-20465707-T-A		not specified	Uncertain significance (Aug 01, 2023)
16-20465718-A-T		not specified	Uncertain significance (Sep 20, 2023)
16-20469541-A-T		not specified	Uncertain significance (Aug 26, 2022)
16-20469557-T-C		not specified	Uncertain significance (Sep 25, 2023)
16-20469580-A-G		not specified	Uncertain significance (Feb 05, 2024)
16-20469590-C-T		not specified	Uncertain significance (Aug 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSM2A	protein_coding	protein_coding	ENST00000573854	13	36209

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.28e-23	0.000533	118166	464	7118	125748	0.0306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.79	411	321	1.28	0.0000168	3732
Missense in Polyphen		132	109.92	1.2008		1331
Synonymous	-1.89	145	119	1.22	0.00000613	1129
Loss of Function	-0.131	34	33.2	1.02	0.00000184	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0454	0.0454
Ashkenazi Jewish	0.0435	0.0440
East Asian	0.208	0.206
Finnish	0.00713	0.00709
European (Non-Finnish)	0.0120	0.0120
Middle Eastern	0.208	0.206
South Asian	0.0202	0.0200
Other	0.0255	0.0256

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 (Consensus)

Recessive Scores

• pRec: 0.0680

Intolerance Scores

• loftool: 0.970
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.51

Haploinsufficiency Scores

• pHI: 0.0621
• hipred: N
• hipred_score: 0.301
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.107

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acsm2
• Phenotype: homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: fatty acid biosynthetic process;acyl-CoA metabolic process;medium-chain fatty-acyl-CoA metabolic process;glucose homeostasis;triglyceride homeostasis
• Cellular component: mitochondrion;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