MTERF2

mitochondrial transcription termination factor 2

Basic information

Region (hg38): 12:106973120-106987163

Previous symbols: [ "MTERFD3" ]

Links

ENSG00000120832 ∙ NCBI:80298 ∙ OMIM:616929 ∙ HGNC:30779 ∙ Uniprot:Q49AM1 ∙ 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 MTERF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTERF2 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			19	1	3	23
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	3

Variants in MTERF2

This is a list of pathogenic ClinVar variants found in the MTERF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-106977567-A-G		not specified	Uncertain significance (Sep 07, 2022)
12-106977666-G-C		not specified	Uncertain significance (Dec 19, 2022)
12-106977728-T-C		not specified	Uncertain significance (Nov 10, 2022)
12-106977751-C-T		not specified	Uncertain significance (Jan 19, 2024)
12-106977759-G-A		not specified	Uncertain significance (Aug 23, 2021)
12-106977770-C-G		not specified	Uncertain significance (Jan 26, 2022)
12-106977948-A-C		not specified	Uncertain significance (Jan 23, 2024)
12-106977948-AAAAG-A			Likely benign (May 17, 2018)
12-106977993-C-T		not specified	Likely benign (Jun 18, 2024)
12-106977996-G-A		not specified	Uncertain significance (Oct 10, 2023)
12-106978047-G-C		not specified	Uncertain significance (Mar 22, 2023)
12-106978111-C-T		not specified	Uncertain significance (Feb 11, 2022)
12-106978215-C-T		not specified	Uncertain significance (Mar 18, 2024)
12-106978228-T-G		not specified	Uncertain significance (Feb 06, 2023)
12-106978237-C-T		not specified	Uncertain significance (Mar 20, 2024)
12-106978333-C-G		not specified	Uncertain significance (Jan 23, 2024)
12-106978381-C-T		not specified	Uncertain significance (Jan 29, 2024)
12-106978405-C-G		not specified	Uncertain significance (Dec 12, 2023)
12-106978461-T-C		not specified	Uncertain significance (Jan 22, 2024)
12-106978472-C-T			Likely benign (Nov 01, 2024)
12-106978473-G-C			Benign (May 09, 2018)
12-106978488-T-C		not specified	Uncertain significance (Jun 06, 2023)
12-106978491-G-A		not specified	Uncertain significance (Nov 06, 2023)
12-106978591-T-C		not specified	Uncertain significance (Mar 20, 2024)
12-106978623-G-A			Benign (May 09, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTERF2	protein_coding	protein_coding	ENST00000552029	1	9876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000246	0.513	125538	1	207	125746	0.000827

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.243	198	189	1.05	0.00000874	2520
Missense in Polyphen		57	54.615	1.0437		803
Synonymous	0.517	67	72.6	0.923	0.00000343	733
Loss of Function	0.749	10	12.9	0.775	6.23e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00835	0.00822
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000299	0.000299
Middle Eastern	0.000163	0.000163
South Asian	0.000787	0.000752
Other	0.000983	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds mitochondrial DNA and plays a role in the regulation of transcription of mitochondrial mRNA and rRNA species. {ECO:0000269|PubMed:16226716, ECO:0000269|PubMed:19366608, ECO:0000269|PubMed:21558281}.

Recessive Scores

• pRec: 0.0782

Intolerance Scores

• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.9

Haploinsufficiency Scores

• pHI: 0.0793
• hipred: N
• hipred_score: 0.197
• ghis: 0.420

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mterf2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription, DNA-templated;termination of mitochondrial transcription
• Cellular component: mitochondrion;mitochondrial nucleoid
• Molecular function: DNA binding;double-stranded DNA binding