ME3

malic enzyme 3

Basic information

Region (hg38): 11:86441107-86672636

Links

ENSG00000151376 ∙ NCBI:10873 ∙ OMIM:604626 ∙ HGNC:6985 ∙ Uniprot:Q16798 ∙ 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 ME3 gene.

• Inborn genetic diseases (20 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ME3 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	1

Variants in ME3

This is a list of pathogenic ClinVar variants found in the ME3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-86441434-C-T		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
11-86442849-C-T		not specified	Uncertain significance (Dec 14, 2022)
11-86442917-T-A		not specified	Uncertain significance (Apr 05, 2023)
11-86446405-T-G		not specified	Uncertain significance (Dec 19, 2022)
11-86447093-G-A		not specified	Uncertain significance (Sep 29, 2022)
11-86447145-C-T		not specified	Uncertain significance (Aug 15, 2023)
11-86447180-G-A		not specified	Uncertain significance (Aug 08, 2022)
11-86448176-C-A		not specified	Uncertain significance (Mar 20, 2023)
11-86449947-G-A		not specified	Uncertain significance (Mar 08, 2024)
11-86449963-C-G		not specified	Uncertain significance (Aug 13, 2021)
11-86449978-G-A		not specified	Uncertain significance (Jul 06, 2021)
11-86450303-C-T		not specified	Uncertain significance (Aug 15, 2023)
11-86450356-C-T		not specified	Uncertain significance (Jan 04, 2022)
11-86465144-C-T		not specified	Uncertain significance (May 05, 2023)
11-86465159-T-C		not specified	Uncertain significance (Feb 28, 2023)
11-86487400-T-G		not specified	Uncertain significance (Dec 11, 2023)
11-86497986-G-A			Benign (Apr 20, 2018)
11-86498009-G-A		not specified	Uncertain significance (May 23, 2023)
11-86508802-T-C		not specified	Uncertain significance (Feb 10, 2022)
11-86508822-C-T		not specified	Uncertain significance (Jan 03, 2022)
11-86508838-C-T		not specified	Uncertain significance (Dec 07, 2021)
11-86556669-G-T		not specified	Uncertain significance (Nov 02, 2021)
11-86671833-G-A		not specified	Uncertain significance (Oct 16, 2023)
11-86671859-G-T		not specified	Uncertain significance (Jun 24, 2022)
11-86671884-C-T		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ME3	protein_coding	protein_coding	ENST00000543262	14	231529

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.51e-13	0.321	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	291	362	0.803	0.0000212	3923
Missense in Polyphen		114	151.97	0.75014		1551
Synonymous	-0.829	164	151	1.09	0.00000984	1225
Loss of Function	1.24	24	31.5	0.762	0.00000177	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000679	0.000662
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000218	0.000217
South Asian	0.000294	0.000294
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Pyruvate metabolism - Homo sapiens (human);Citric acid cycle (TCA cycle);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: 0.184

Intolerance Scores

• loftool: 0.799
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.88

Haploinsufficiency Scores

• pHI: 0.219
• hipred: Y
• hipred_score: 0.563
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.130

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Me3
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: pyruvate metabolic process;tricarboxylic acid cycle;malate metabolic process;aerobic respiration;oxidation-reduction process;oxygen metabolic process
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: malic enzyme activity;malate dehydrogenase (decarboxylating) (NAD+) activity;malate dehydrogenase (decarboxylating) (NADP+) activity;oxaloacetate decarboxylase activity;metal ion binding;cofactor binding;NAD binding