TEFM
protein-codingtranscription elongation factor, mitochondrial
Gene summary
Enables transcription elongation factor activity. Involved in positive regulation of mitochondrial transcription and regulation of oxidative phosphorylation. Located in mitochondrial nucleoid. Part of ribonucleoprotein complex. Implicated in combined oxidative phosphorylation deficiency. [provided by Alliance of Genome Resources, Jul 2025]
- C17orf42
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0957537
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0957537
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0957537
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TEFM variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024683.4. 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 | 2 | 3 | |||
| missense | 51 | 3 | 54 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 52 | 5 | 0 | 57 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078959.3 | 4 | MANE Select | |
| Ensembl | ENSP00000462963.1 | 4 | MANE Select | |
| Ensembl | ENSP00000306574.5 | 3 | Standard | |
| Ensembl | ENSP00000462973.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- oxidative phosphorylation
- mitochondrial DNA replication
- mitochondrial transcription
- transcription elongation from mitochondrial promoter
Molecular Function
- RNA binding
- protein binding
- crossover junction endodeoxyribonuclease activity
- DNA polymerase processivity factor activity
Cellular Component
- mitochondrion
- mitochondrial matrix
- mitochondrial nucleoid
- ribonucleoprotein complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000581216
- Coding exons
- 4
- Length
- 9485
- Individuals with no LoFs
- 124771
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 124793
- p
- 0.0000882
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.584 | 173 | 196 | 0.883 | 0.0000106 | 2347 |
| Missense (PolyPhen) | 43 | 57.64 | 0.74601 | 737 | ||
| Synonymous | 1.86 | 54 | 74.4 | 0.726 | 0.00000392 | 697 |
| Loss of Function | 2.86 | 3 | 14.9 | 0.201 | 8.44e-7 | 184 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000090 | 0.000088 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcription elongation factor which increases mitochondrial RNA polymerase processivity. Regulates transcription of the mitochondrial genome, including genes important for the oxidative phosphorylation machinery. {ECO:0000269|PubMed:21278163}.;
Recessive Scores
- pRec
- 0.0741
Intolerance Scores
- RVIS EVS
- -0.09
- RVIS percentile EVS
- 46.74
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |