ACSM2B

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

Basic information

Region (hg38): 16:20536226-20576427

Previous symbols: [ "ACSM2" ]

Links

ENSG00000066813 ∙ NCBI:348158 ∙ OMIM:614359 ∙ HGNC:30931 ∙ Uniprot:Q68CK6 ∙ 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 ACSM2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSM2B 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			22	1	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	3

Variants in ACSM2B

This is a list of pathogenic ClinVar variants found in the ACSM2B region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20540726-G-T		not specified	Uncertain significance (Nov 27, 2023)
16-20542945-A-T		not specified	Uncertain significance (Dec 07, 2022)
16-20542963-G-T		not specified	Uncertain significance (Dec 21, 2022)
16-20543162-C-T		not specified	Uncertain significance (Oct 18, 2021)
16-20543163-G-A		not specified	Uncertain significance (Jun 24, 2022)
16-20543195-T-G		not specified	Uncertain significance (Jul 11, 2023)
16-20543246-G-A		not specified	Uncertain significance (Mar 01, 2023)
16-20545191-G-C		not specified	Uncertain significance (Dec 13, 2022)
16-20545254-A-G		not specified	Uncertain significance (Jun 28, 2023)
16-20545257-A-T		not specified	Uncertain significance (Oct 26, 2022)
16-20546419-G-A		not specified	Uncertain significance (May 15, 2024)
16-20546447-T-C		not specified	Uncertain significance (May 18, 2022)
16-20546455-G-A		not specified	Uncertain significance (Apr 07, 2022)
16-20548144-T-G		not specified	Uncertain significance (Sep 15, 2021)
16-20548397-G-C		not specified	Uncertain significance (Mar 31, 2024)
16-20548432-A-G			Benign (Oct 17, 2017)
16-20548455-T-C			Benign (Oct 17, 2017)
16-20552222-T-G			Benign (Aug 18, 2017)
16-20553787-T-C		not specified	Uncertain significance (Oct 03, 2022)
16-20553871-A-T		not specified	Uncertain significance (Aug 02, 2021)
16-20553920-A-C		not specified	Likely benign (Jan 18, 2023)
16-20555412-C-T		not specified	Uncertain significance (Mar 31, 2023)
16-20555450-G-T		not specified	Uncertain significance (Aug 24, 2022)
16-20559353-T-C		not specified	Uncertain significance (Jul 09, 2021)
16-20564688-T-A		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSM2B	protein_coding	protein_coding	ENST00000329697	13	40202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.27e-26	0.0000954	125427	2	319	125748	0.00128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.98	417	318	1.31	0.0000168	3728
Missense in Polyphen		152	107.68	1.4116		1337
Synonymous	-2.61	152	116	1.31	0.00000599	1114
Loss of Function	-0.430	37	34.3	1.08	0.00000197	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00917	0.00912
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00114	0.00114
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000847	0.000835
Middle Eastern	0.00114	0.00114
South Asian	0.000756	0.000752
Other	0.000663	0.000652

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). {ECO:0000269|PubMed:12616642}.
• Pathway: Butanoate metabolism - Homo sapiens (human);Valproic Acid Pathway, Pharmacokinetics;Phenylacetate Metabolism;Conjugation of benzoate with glycine;Conjugation of phenylacetate with glutamine;Conjugation of salicylate with glycine;Conjugation of carboxylic acids;Amino Acid conjugation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism (Consensus)

Recessive Scores

• pRec: 0.0729

Intolerance Scores

• loftool: 0.939
• rvis_EVS: 0.56
• rvis_percentile_EVS: 81.71

Haploinsufficiency Scores

• pHI: 0.0777
• hipred: N
• hipred_score: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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;xenobiotic metabolic process
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: molecular_function;acyl-CoA ligase activity;fatty-acyl-CoA synthase activity;ATP binding;fatty acid ligase activity;CoA-ligase activity;metal ion binding;butyrate-CoA ligase activity