MTERF3

mitochondrial transcription termination factor 3

Basic information

Region (hg38): 8:96239398-96261610

Previous symbols: [ "MTERFD1" ]

Links

ENSG00000156469 ∙ NCBI:51001 ∙ OMIM:616930 ∙ HGNC:24258 ∙ Uniprot:Q96E29 ∙ 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 MTERF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTERF3 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			20			20
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	20	0	1

Variants in MTERF3

This is a list of pathogenic ClinVar variants found in the MTERF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-96239553-A-G		not specified	Uncertain significance (Aug 01, 2023)
8-96243980-G-A		not specified	Uncertain significance (May 09, 2022)
8-96243984-C-T		not specified	Uncertain significance (Sep 17, 2021)
8-96244035-T-C		not specified	Uncertain significance (Nov 10, 2022)
8-96245865-T-C		not specified	Uncertain significance (Jul 07, 2022)
8-96245894-G-C		not specified	Uncertain significance (May 08, 2024)
8-96245912-C-T		not specified	Uncertain significance (May 04, 2023)
8-96245925-C-G		not specified	Uncertain significance (May 08, 2024)
8-96246353-T-A		not specified	Uncertain significance (Feb 27, 2023)
8-96250946-G-C		not specified	Uncertain significance (Jun 06, 2023)
8-96251090-C-A		not specified	Uncertain significance (May 25, 2022)
8-96256964-A-G		not specified	Uncertain significance (Dec 07, 2021)
8-96256985-G-C		not specified	Uncertain significance (Aug 08, 2023)
8-96257013-G-A		not specified	Uncertain significance (Nov 30, 2022)
8-96258359-T-C		not specified	Uncertain significance (Mar 15, 2024)
8-96258363-G-T		not specified	Uncertain significance (Jan 23, 2023)
8-96258398-G-A		not specified	Uncertain significance (Oct 05, 2021)
8-96258510-A-G		not specified	Uncertain significance (Feb 28, 2023)
8-96258521-C-G		not specified	Uncertain significance (Jan 08, 2024)
8-96258572-C-A		not specified	Uncertain significance (Sep 26, 2022)
8-96258617-T-C		not specified	Uncertain significance (May 27, 2022)
8-96258667-T-C		not specified	Uncertain significance (Dec 15, 2022)
8-96258669-T-C		not specified	Uncertain significance (Oct 16, 2023)
8-96261601-C-G			Benign (Jun 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTERF3	protein_coding	protein_coding	ENST00000287025	7	22213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.03e-8	0.321	125662	0	84	125746	0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.117	215	210	1.02	0.00000995	2762
Missense in Polyphen		66	67.082	0.98388		934
Synonymous	0.625	68	74.9	0.908	0.00000358	783
Loss of Function	0.704	14	17.1	0.816	7.91e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000912	0.000910
Ashkenazi Jewish	0.00	0.00
East Asian	0.000442	0.000435
Finnish	0.0000956	0.0000924
European (Non-Finnish)	0.000225	0.000220
Middle Eastern	0.000442	0.000435
South Asian	0.000905	0.000850
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds promoter DNA and regulates initiation of transcription (PubMed:17662942). Required for normal mitochondrial transcription and translation, and for normal assembly of mitochondrial respiratory complexes. Required for normal mitochondrial function (By similarity). Maintains 16S rRNA levels and functions in mitochondrial ribosome assembly by regulating the biogenesis of the 39S ribosomal subunit (By similarity). {ECO:0000250|UniProtKB:Q8R3J4, ECO:0000269|PubMed:17662942}.
• Pathway: Mitochondrial Gene Expression;Pink/Parkin Mediated Mitophagy;Mitophagy (Consensus)

Recessive Scores

• pRec: 0.0891

Intolerance Scores

• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.55

Haploinsufficiency Scores

• pHI: 0.454
• hipred: N
• hipred_score: 0.197
• ghis: 0.510

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Mterf3
• Phenotype: embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); muscle phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: mitochondrial transcription;macroautophagy;mitochondrial translation;negative regulation of transcription, DNA-templated;mitochondrial ribosome assembly
• Cellular component: nucleoplasm;mitochondrion;mitochondrial outer membrane
• Molecular function: double-stranded DNA binding;protein binding;transcription regulatory region DNA binding