MCAT

malonyl-CoA-acyl carrier protein transacylase

Basic information

Region (hg38): 22:43132209-43143398

Links

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

Phenotypes

GenCC

Source: genCC

• optic atrophy 15 (Limited), mode of inheritance: AR
• 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.

• not_specified (50 variants)
• not_provided (9 variants)
• Retinal_dystrophy (7 variants)
• Optic_atrophy_15 (2 variants)
• MCAT-related_condition (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. These statistics are base on transcript: NM_000173467.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense	1		53	6	2	62
nonsense						0
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)	1					1
Total	2	0	55	8	3

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
		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

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

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