MTERF3
protein-codingmitochondrial transcription termination factor 3
Gene summary
Enables transcription cis-regulatory region binding activity. Involved in negative regulation of DNA-templated transcription. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Jun 2026]
- MTERFD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~22.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to MTERF3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015942.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 49 | 1 | 50 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 53 | 1 | 0 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057026.3 | 7 | MANE Select | |
| Ensembl | ENSP00000287025.3 | 7 | MANE Select | |
| RefSeq | NP_001273572.1 | 7 | Standard | |
| RefSeq | NP_001349893.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Mitochondrial Gene Expression
- Pink/Parkin Mediated Mitophagy
- Mitophagy
Biological Process
- mitochondrial transcription
- macroautophagy
- mitochondrial translation
- negative regulation of transcription, DNA-templated
- mitochondrial ribosome assembly
Molecular Function
- double-stranded DNA binding
- protein binding
- transcription regulatory region DNA binding
Cellular Component
- nucleoplasm
- mitochondrion
- mitochondrial outer membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000287025
- Coding exons
- 7
- Length
- 22213
- Individuals with no LoFs
- 125662
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 84
- Defined
- 125746
- p
- 0.000334
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.117 | 215 | 210 | 1.02 | 0.00000995 | 2762 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.00048 | 0.00046 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.000096 | 0.000092 | rare |
| European (Non-Finnish) | 0.00022 | 0.00022 | rare |
| South Asian | 0.00091 | 0.00085 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.0891
Intolerance Scores
- RVIS EVS
- 0.55
- RVIS percentile EVS
- 81.55
Essentials
- Essential (gene trap)
- H