MTERF4

mitochondrial transcription termination factor 4

Basic information

Region (hg38): 2:241072169-241102332

Previous symbols: [ "MTERFD2" ]

Links

ENSG00000122085 ∙ NCBI:130916 ∙ OMIM:615393 ∙ HGNC:28785 ∙ Uniprot:Q7Z6M4 ∙ 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 MTERF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTERF4 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			17	4		21
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	18	4	0

Variants in MTERF4

This is a list of pathogenic ClinVar variants found in the MTERF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-241073289-G-A		not specified	Uncertain significance (Jul 06, 2021)
2-241073311-A-G		not specified	Uncertain significance (Apr 15, 2024)
2-241073344-A-G			Benign (Nov 20, 2018)
2-241073358-A-G		not specified	Uncertain significance (May 11, 2022)
2-241073361-G-A		not specified	Uncertain significance (May 25, 2022)
2-241073367-G-A			Benign (Nov 20, 2018)
2-241081697-G-A		not specified	Uncertain significance (Dec 20, 2021)
2-241081714-C-T			Likely benign (Feb 01, 2023)
2-241081761-G-A		not specified	Uncertain significance (Apr 12, 2022)
2-241082272-C-T			Likely benign (May 09, 2018)
2-241087412-T-C		not specified	Uncertain significance (Apr 06, 2022)
2-241088385-C-T		not specified	Uncertain significance (Dec 04, 2024)
2-241096063-C-T		not specified	Uncertain significance (Oct 28, 2023)
2-241096078-T-C		not specified	Uncertain significance (Dec 27, 2023)
2-241096092-T-C		not specified	Uncertain significance (Dec 02, 2024)
2-241096116-T-A		not specified	Uncertain significance (Aug 07, 2024)
2-241096152-G-A		not specified	Uncertain significance (Oct 21, 2021)
2-241096368-G-A		not specified	Uncertain significance (Oct 14, 2023)
2-241097277-C-T		not specified	Uncertain significance (Aug 16, 2022)
2-241097298-T-C		not specified	Uncertain significance (Nov 14, 2024)
2-241097337-T-G		not specified	Uncertain significance (Aug 14, 2023)
2-241097350-G-C		not specified	Likely benign (Oct 12, 2022)
2-241097362-C-T		not specified	Uncertain significance (Aug 30, 2021)
2-241097424-T-C		not specified	Uncertain significance (Dec 22, 2023)
2-241099416-T-C		not specified	Likely benign (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTERF4	protein_coding	protein_coding	ENST00000391980	4	30164

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000340	0.824	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.561	188	211	0.891	0.0000115	2533
Missense in Polyphen		50	55.788	0.89626		707
Synonymous	-0.429	88	83.0	1.06	0.00000482	709
Loss of Function	1.29	9	14.2	0.632	7.57e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000378	0.000378
Middle Eastern	0.000109	0.000109
South Asian	0.0000981	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of mitochondrial ribosome biogenesis and translation. Binds to mitochondrial ribosomal RNAs 16S, 12S and 7S and targets NSUN4 RNA methyltransferase to the mitochondrial large ribosomal subunit (39S). {ECO:0000269|PubMed:21531335}.
• Pathway: rRNA processing;rRNA modification in the mitochondrion;Metabolism of RNA;rRNA processing in the mitochondrion (Consensus)

Recessive Scores

• pRec: 0.0778

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.0958
• hipred: N
• hipred_score: 0.123
• ghis: 0.511

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Mterf4
• Phenotype: growth/size/body region phenotype; muscle phenotype; cellular 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); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription, DNA-templated;mitochondrial transcription;protein targeting to mitochondrion;heart development;rRNA methylation;mitochondrial translation;camera-type eye development;mitochondrial ribosome assembly
• Cellular component: mitochondrion;mitochondrial matrix;mitochondrial large ribosomal subunit;cytosol
• Molecular function: double-stranded DNA binding;protein binding;rRNA binding