ME1

malic enzyme 1

Basic information

Region (hg38): 6:83210402-83431051

Links

ENSG00000065833 ∙ NCBI:4199 ∙ OMIM:154250 ∙ HGNC:6983 ∙ Uniprot:P48163 ∙ 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 ME1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ME1 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			24			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	24	0	1

Variants in ME1

This is a list of pathogenic ClinVar variants found in the ME1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-83211959-C-T		not specified	Uncertain significance (Mar 01, 2023)
6-83211968-A-G		not specified	Uncertain significance (Dec 02, 2022)
6-83211994-T-A		not specified	Uncertain significance (Dec 11, 2023)
6-83216581-C-A		not specified	Uncertain significance (Jan 19, 2022)
6-83223772-G-A			Benign (Apr 10, 2018)
6-83223833-G-C		not specified	Uncertain significance (Mar 02, 2023)
6-83223851-T-C		not specified	Uncertain significance (Dec 20, 2023)
6-83223857-T-G		not specified	Uncertain significance (Jul 30, 2023)
6-83223880-A-T		not specified	Uncertain significance (May 10, 2024)
6-83223890-G-A		not specified	Uncertain significance (Dec 05, 2022)
6-83227339-G-A		not specified	Uncertain significance (Oct 05, 2021)
6-83227412-G-A		not specified	Uncertain significance (Jan 18, 2023)
6-83228891-T-C		not specified	Uncertain significance (May 04, 2022)
6-83228915-G-A		not specified	Uncertain significance (Dec 22, 2023)
6-83228928-G-A		not specified	Uncertain significance (Jan 18, 2023)
6-83237747-C-G		not specified	Uncertain significance (Jan 17, 2024)
6-83237776-G-A		not specified	Uncertain significance (Dec 17, 2021)
6-83239564-G-A		not specified	Uncertain significance (Jan 30, 2024)
6-83253697-T-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
6-83315379-C-T		not specified	Uncertain significance (Feb 12, 2024)
6-83346309-C-A		not specified	Uncertain significance (Jul 13, 2021)
6-83398376-C-T		not specified	Uncertain significance (Nov 21, 2022)
6-83398387-A-C		not specified	Uncertain significance (Nov 15, 2021)
6-83398435-C-T		not specified	Uncertain significance (Oct 03, 2022)
6-83398444-C-G		not specified	Uncertain significance (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ME1	protein_coding	protein_coding	ENST00000369705	14	220690

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.20e-14	0.129	124543	4	1200	125747	0.00480

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.287	312	298	1.05	0.0000150	3709
Missense in Polyphen		111	117.99	0.94073		1408
Synonymous	-0.212	106	103	1.03	0.00000505	1096
Loss of Function	0.857	23	27.9	0.825	0.00000137	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00407	0.00382
Ashkenazi Jewish	0.000223	0.000198
East Asian	0.000680	0.000653
Finnish	0.00606	0.00593
European (Non-Finnish)	0.00873	0.00784
Middle Eastern	0.000680	0.000653
South Asian	0.00303	0.00242
Other	0.00307	0.00261

dbNSFP

Source: dbNSFP

• Pathway: Pyruvate metabolism - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Pyruvate Dehydrogenase Complex Deficiency;Transfer of Acetyl Groups into Mitochondria;Primary hyperoxaluria II, PH2;Pyruvate kinase deficiency;Leigh Syndrome;Glutaminolysis and Cancer;Pyruvate Metabolism;Pyruvate Decarboxylase E1 Component Deficiency (PDHE1 Deficiency);Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Nuclear Receptors Meta-Pathway;NRF2 pathway;PPAR signaling pathway;Pathways in clear cell renal cell carcinoma;mechanism of gene regulation by peroxisome proliferators via ppara;Pyruvate metabolism;Pyruvate metabolism and Citric Acid (TCA) cycle;Glycolysis Gluconeogenesis;The citric acid (TCA) cycle and respiratory electron transport;Glycolysis and Gluconeogenesis;Metabolism;Pyruvate metabolism (Consensus)

Recessive Scores

• pRec: 0.198

Intolerance Scores

• loftool: 0.930
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.82

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.389
• ghis: 0.455

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.780

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Me1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;pyruvate metabolic process;malate metabolic process;NADP biosynthetic process;response to hormone;response to carbohydrate;regulation of lipid metabolic process;electron transport chain;protein tetramerization;regulation of NADP metabolic process
• Cellular component: mitochondrion;cytosol
• Molecular function: malic enzyme activity;malate dehydrogenase (decarboxylating) (NAD+) activity;malate dehydrogenase (decarboxylating) (NADP+) activity;oxaloacetate decarboxylase activity;electron transfer activity;manganese ion binding;ADP binding;NADP binding;NAD binding