MCAT

malonyl-CoA-acyl carrier protein transacylase

Basic information

Region (hg38): 22:43132208-43143398

Links

ENSG00000100294 ∙ NCBI:27349 ∙ OMIM:614479 ∙ HGNC:29622 ∙ Uniprot:Q8IVS2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive optic atrophy (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Optic atrophy 15	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	31915829; 33918393

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MCAT gene.

• Inborn genetic diseases (11 variants)
• not provided (7 variants)
• - (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MCAT 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					1	1
missense			12	2	2	16
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	12	2	4

Variants in MCAT

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

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

Position	Type	Phenotype	Significance	ClinVar
22-43133055-C-A			Benign (Jun 12, 2018)
22-43133088-C-G			Benign (Feb 08, 2018)
22-43133128-A-G		not specified	Uncertain significance (Mar 07, 2023)
22-43133152-C-T		not specified	Uncertain significance (Dec 28, 2023)
22-43133177-C-T			Uncertain significance (Jul 01, 2021)
22-43133213-C-T		not specified	Uncertain significance (Dec 28, 2023)
22-43133371-G-A		not specified	Uncertain significance (Apr 25, 2023)
22-43133387-C-T		not specified	Uncertain significance (Dec 17, 2023)
22-43133393-C-T		Optic atrophy 15	Pathogenic (Nov 13, 2023)
22-43133404-G-A			Uncertain significance (Nov 13, 2023)
22-43133438-T-C		not specified	Likely benign (Nov 06, 2023)
22-43133441-G-A		not specified	Uncertain significance (Mar 07, 2024)
22-43137099-C-G			Benign (Feb 25, 2018)
22-43137131-C-T		not specified	Uncertain significance (Aug 02, 2022)
22-43137157-A-G		not specified	Uncertain significance (Jul 16, 2021)
22-43137175-C-T		not specified	Likely benign (Dec 28, 2022)
22-43137176-G-A		-	no classification for the single variant (-)
22-43141086-T-C			Benign (May 01, 2023)
22-43141251-T-C		Optic atrophy 15	Pathogenic (Nov 13, 2023)
22-43143021-G-A		not specified	Uncertain significance (Jan 04, 2024)
22-43143060-C-A		not specified	Uncertain significance (Jan 10, 2023)
22-43143107-A-C		-	no classification for the single variant (-)
22-43143114-G-C			Likely benign (Nov 01, 2023)
22-43143143-C-G		not specified	Uncertain significance (May 02, 2023)
22-43143173-G-A		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MCAT	protein_coding	protein_coding	ENST00000290429	4	11189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000306	0.819	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.291	202	214	0.944	0.0000120	2471
Missense in Polyphen		83	89.661	0.9257		996
Synonymous	-0.767	105	95.5	1.10	0.00000609	820
Loss of Function	1.19	7	11.3	0.619	5.68e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000550	0.000535
Ashkenazi Jewish	0.00	0.00
East Asian	0.000173	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000232	0.000229
Middle Eastern	0.000173	0.000163
South Asian	0.0000980	0.0000980
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the transfer of a malonyl moiety from malonyl- CoA to the free thiol group of the phosphopantetheine arm of the mitochondrial ACP protein (NDUFAB1). This suggests the existence of the biosynthesis of fatty acids in mitochondria. {ECO:0000269|PubMed:12882974}.
• Pathway: Fatty acid biosynthesis - Homo sapiens (human);Metabolism of lipids;Mitochondrial Fatty Acid Beta-Oxidation;Metabolism;Fatty acid metabolism;fatty acid biosynthesis initiation (Consensus)

Recessive Scores

• pRec: 0.318

Intolerance Scores

• loftool: 0.538
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.34

Haploinsufficiency Scores

• pHI: 0.222
• hipred: N
• hipred_score: 0.180
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.695

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mcat
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region 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); muscle phenotype; immune system phenotype; homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; digestive/alimentary phenotype; skeleton phenotype

Gene ontology

• Biological process: fatty acid biosynthetic process;fatty acid beta-oxidation
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: RNA binding;fatty acid synthase activity;[acyl-carrier-protein] S-malonyltransferase activity