MECR

mitochondrial trans-2-enoyl-CoA reductase

Basic information

Region (hg38): 1:29192657-29230942

Links

ENSG00000116353

∙ NCBI:51102 ∙ OMIM:608205 ∙ HGNC:19691 ∙ Uniprot:Q9BV79 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

dystonia, childhood-onset, with optic atrophy and basal ganglia abnormalities (Strong), mode of inheritance: AR
Leigh syndrome (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Dystonia, childhood-onset, with optic atrophy and basal ganglia abnormalities; Optic atrophy 16	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	Audiologic/Otolaryngologic; Neurologic; Ophthalmologic	27817865; 37734847

ClinVar

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

not_provided (269 variants)
Inborn_genetic_diseases (53 variants)
Dystonia,_childhood-onset,_with_optic_atrophy_and_basal_ganglia_abnormalities (15 variants)
MECR-related_disorder (10 variants)
Childhood_Onset_Dystonias (6 variants)
Optic_atrophy (6 variants)
Optic_atrophy_16 (4 variants)
not_specified (2 variants)
Mitochondrial_disease (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MECR gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016011.5. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				99 clinvar		99
missense	2 clinvar	3 clinvar	79 clinvar	13 clinvar		97
nonsense	8 clinvar	1 clinvar	1 clinvar			10
start loss						0
frameshift	11 clinvar					11
splice donor/acceptor (+/-2bp)		6 clinvar				6
Total	21	10	80	112	0

Highest pathogenic variant AF is 0.0000805599

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MECR	protein_coding	protein_coding	ENST00000263702	10	38070

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000223	0.980	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.111	214	219	0.979	0.0000120	2386
Missense in Polyphen		39	47.757	0.81664		559
Synonymous	-0.773	98	88.7	1.10	0.00000515	778
Loss of Function	2.09	11	21.5	0.512	0.00000117	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000548	0.000548
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.000116	0.000109
South Asian	0.000336	0.000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis (fatty acid synthesis type II). Fatty acid chain elongation in mitochondria uses acyl carrier protein (ACP) as an acyl group carrier, but the enzyme accepts both ACP and CoA thioesters as substrates in vitro. Has a preference for short and medium chain substrates, including trans-2-hexenoyl-CoA (C6), trans-2-decenoyl-CoA (C10), and trans- 2-hexadecenoyl-CoA (C16). {ECO:0000269|PubMed:18479707, ECO:0000269|PubMed:27817865}.;
Pathway: Fatty acid elongation - Homo sapiens (human);Long-chain-3-hydroxyacyl-coa dehydrogenase deficiency (LCHAD);Fatty Acid Elongation In Mitochondria;Fatty Acid Biosynthesis;Liver steatosis AOP;Metabolism of lipids;Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA;mitochondrial fatty acid beta-oxidation of saturated fatty acids;Mitochondrial Fatty Acid Beta-Oxidation;Saturated fatty acids beta-oxidation;Metabolism;Fatty acid metabolism (Consensus)

Recessive Scores

pRec: 0.111

Intolerance Scores

loftool: 0.870
rvis_EVS: 0.71
rvis_percentile_EVS: 85.63

Haploinsufficiency Scores

pHI: 0.416
hipred: N
hipred_score: 0.443
ghis: 0.422

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0583

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mecr
Phenotype

Gene ontology

Biological process: fatty acid metabolic process;fatty acid biosynthetic process;fatty acid beta-oxidation
Cellular component: nucleus;mitochondrion;mitochondrial matrix
Molecular function: trans-2-enoyl-CoA reductase (NADPH) activity