MPC2

mitochondrial pyruvate carrier 2, the group of Solute carrier family 54, mitochondrial pyruvate carriers

Basic information

Region (hg38): 1:167916674-167937072

Previous symbols: [ "BRP44" ]

Links

ENSG00000143158 ∙ NCBI:25874 ∙ OMIM:614737 ∙ HGNC:24515 ∙ Uniprot:O95563 ∙ 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 MPC2 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPC2 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						0
missense			2			2
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	3	0	0

Variants in MPC2

This is a list of pathogenic ClinVar variants found in the MPC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-167920069-G-A		not specified	Uncertain significance (Jan 04, 2022)
1-167935811-C-G		not specified	Uncertain significance (May 25, 2022)
1-167936982-C-T		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPC2	protein_coding	protein_coding	ENST00000367846	5	20312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.635	0.359	125686	1	2	125689	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.985	42	64.2	0.654	0.00000282	799
Missense in Polyphen		10	18.055	0.55385		263
Synonymous	-0.712	27	22.7	1.19	0.00000102	244
Loss of Function	2.20	1	7.49	0.134	3.22e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000132	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000949	0.00000880
Middle Eastern	0.000132	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the uptake of pyruvate into mitochondria. {ECO:0000269|PubMed:22628558}.
• Pathway: Glycolysis and Gluconeogenesis;Pyruvate metabolism;Pyruvate metabolism and Citric Acid (TCA) cycle;The citric acid (TCA) cycle and respiratory electron transport;Metabolism (Consensus)

Recessive Scores

• pRec: 0.0961

Intolerance Scores

• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.79

Haploinsufficiency Scores

• pHI: 0.220
• hipred: N
• hipred_score: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mpc2
• Phenotype: 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); endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: mitochondrial pyruvate transmembrane transport;positive regulation of insulin secretion involved in cellular response to glucose stimulus;mitochondrial acetyl-CoA biosynthetic process from pyruvate
• Cellular component: nucleus;mitochondrion;integral component of mitochondrial inner membrane
• Molecular function: pyruvate transmembrane transporter activity