MTCH2

mitochondrial carrier 2, the group of Solute carrier family 25

Basic information

Region (hg38): 11:47617314-47642607

Links

ENSG00000109919 ∙ NCBI:23788 ∙ OMIM:613221 ∙ HGNC:17587 ∙ Uniprot:Q9Y6C9 ∙ 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 MTCH2 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTCH2 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in MTCH2

This is a list of pathogenic ClinVar variants found in the MTCH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47618858-C-A		not specified	Uncertain significance (Mar 16, 2023)
11-47622768-C-G		not specified	Uncertain significance (Aug 08, 2022)
11-47625698-T-C		not specified	Uncertain significance (Aug 15, 2023)
11-47628999-C-T		not specified	Uncertain significance (Oct 26, 2022)
11-47630583-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-47631051-C-T		not specified	Uncertain significance (Nov 10, 2022)
11-47631085-T-C		not specified	Uncertain significance (Jan 03, 2024)
11-47631695-A-G		not specified	Uncertain significance (Jun 18, 2021)
11-47634724-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-47635549-C-T		not specified	Uncertain significance (Oct 26, 2021)
11-47638773-C-T		not specified	Uncertain significance (Feb 14, 2023)
11-47638975-A-G		not specified	Uncertain significance (Aug 21, 2023)
11-47638981-C-T		not specified	Uncertain significance (Nov 18, 2022)
11-47638996-A-C		not specified	Uncertain significance (May 23, 2023)
11-47639003-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-47639023-A-G		not specified	Uncertain significance (Dec 16, 2021)
11-47639026-G-A		not specified	Uncertain significance (Dec 14, 2023)
11-47642420-T-G		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTCH2	protein_coding	protein_coding	ENST00000302503	13	25309

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0319	0.968	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	128	173	0.742	0.00000935	1948
Missense in Polyphen		22	47.614	0.46205		573
Synonymous	0.948	50	59.3	0.843	0.00000320	586
Loss of Function	3.13	7	23.3	0.300	0.00000134	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The substrate transported is not yet known. Induces mitochondrial depolarization.

Intolerance Scores

• loftool: 0.432
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.404
• hipred: N
• hipred_score: 0.426
• ghis: 0.486

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.716

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mtch2
• Phenotype: embryo phenotype; liver/biliary system 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); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: mtch2
• Affected structure: visceral fat
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: positive regulation of apoptotic process;protein localization to mitochondrion
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;membrane;integral component of membrane