MTERF4

gene
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Also known as MGC61716

Summary

MTERF4 (mitochondrial transcription termination factor 4, HGNC:28785) is a protein-coding gene on chromosome 2q37.3, encoding Transcription termination factor 4, mitochondrial (Q7Z6M4). Regulator of mitochondrial ribosome biogenesis and translation. It is a selective cancer dependency (DepMap: 13.7% of cell lines).

Enables rRNA binding activity. Predicted to be involved in mitochondrial ribosome assembly and mitochondrial transcription. Predicted to act upstream of or within several processes, including camera-type eye development; protein targeting to mitochondrion; and ribosome assembly. Located in cytosol and mitochondrion. Part of mitochondrial large ribosomal subunit.

Source: NCBI Gene 130916 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 273 total — 1 pathogenic
  • Cancer dependency (DepMap): dependent in 13.7% of screened cell lines
  • MANE Select transcript: NM_182501

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28785
Approved symbolMTERF4
Namemitochondrial transcription termination factor 4
Location2q37.3
Locus typegene with protein product
StatusApproved
AliasesMGC61716
Ensembl geneENSG00000122085
Ensembl biotypeprotein_coding
OMIM615393
Entrez130916

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 13 protein_coding, 6 protein_coding_CDS_not_defined, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000241527, ENST00000391980, ENST00000401626, ENST00000406593, ENST00000407095, ENST00000414146, ENST00000424798, ENST00000434791, ENST00000439144, ENST00000449133, ENST00000455202, ENST00000460915, ENST00000464344, ENST00000475860, ENST00000476564, ENST00000479205, ENST00000480298, ENST00000488567, ENST00000493169, ENST00000495694, ENST00000496878, ENST00000614476, ENST00000902117, ENST00000923999

RefSeq mRNA: 3 — MANE Select: NM_182501 NM_001330179, NM_001330180, NM_182501

CCDS: CCDS2544, CCDS82584

Canonical transcript exons

ENST00000391980 — 4 exons

ExonStartEnd
ENSE00000827773241099396241099894
ENSE00001510314241095571241096438
ENSE00001601042241102253241102287
ENSE00003694390241097243241097427

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 96.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.6596 / max 361.1099, expressed in 1813 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
3487928.65961813

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489096.25gold quality
sural nerveUBERON:001548896.25gold quality
cerebellar hemisphereUBERON:000224595.95gold quality
cerebellar cortexUBERON:000212995.76gold quality
left lobe of thyroid glandUBERON:000112095.71gold quality
right lobe of thyroid glandUBERON:000111995.67gold quality
thyroid glandUBERON:000204695.02gold quality
left ovaryUBERON:000211994.18gold quality
gastrocnemiusUBERON:000138893.89gold quality
tendon of biceps brachiiUBERON:000818893.68gold quality
right ovaryUBERON:000211893.57gold quality
muscle of legUBERON:000138393.55gold quality
parotid glandUBERON:000183193.55gold quality
hindlimb stylopod muscleUBERON:000425293.52gold quality
cerebellumUBERON:000203793.40gold quality
body of pancreasUBERON:000115093.23gold quality
lymph nodeUBERON:000002993.20gold quality
small intestine Peyer’s patchUBERON:000345493.15gold quality
body of uterusUBERON:000985393.05gold quality
right uterine tubeUBERON:000130292.87gold quality
tibial nerveUBERON:000132392.70gold quality
left uterine tubeUBERON:000130392.41gold quality
colonic epitheliumUBERON:000039792.39gold quality
islet of LangerhansUBERON:000000692.34gold quality
minor salivary glandUBERON:000183092.18gold quality
esophagus mucosaUBERON:000246992.12gold quality
saliva-secreting glandUBERON:000104492.08gold quality
lower esophagus mucosaUBERON:003583492.07gold quality
right frontal lobeUBERON:000281091.97gold quality
endocervixUBERON:000045891.89gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting MTERF4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-477599.9875.006394
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-590-3P99.9674.346478
HSA-MIR-335-3P99.9373.364958
HSA-MIR-129799.9173.413162
HSA-MIR-26A-5P99.7873.522303
HSA-MIR-26B-5P99.7873.512305
HSA-MIR-446599.7172.562096
HSA-MIR-580-3P99.6769.231841
HSA-MIR-7152-5P99.6069.332094
HSA-MIR-516A-3P99.4667.961378
HSA-MIR-516B-3P99.4667.961378
HSA-MIR-7162-5P99.4668.081368
HSA-MIR-653-5P99.4667.351300
HSA-MIR-431199.3170.473041
HSA-MIR-125399.1267.081688
HSA-MIR-548AS-3P99.1269.122294
HSA-MIR-4699-5P98.9967.501210
HSA-MIR-1288-5P98.8567.01734
HSA-MIR-770598.6967.47543
HSA-MIR-548AT-3P98.3764.98580
HSA-MIR-548AY-3P98.3765.14562
HSA-MIR-506-5P98.0267.411065
HSA-MIR-125A-3P97.0466.92902
HSA-MIR-71196.6065.75528
HSA-MIR-55495.2066.98341

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 13.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • analysis of the 3D crystal structure of the human MTERF4-NSUN4 complex (PMID:22949673)
  • The overexpression of MTERF4 induced a significant increase in the levels of APP protein and secreted Abeta 42 in HEK293-APPswe cells compared with control cells these results suggest that MTERF4 promotes the amyloidogenic processing of APP by inhibiting ADAM10 in HEK293-APPswe cells; therefore, MTERF4 may play an important role in the pathogenesis of Alzheimer’s disease. (PMID:27894840)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomterf4ENSDARG00000079124
mus_musculusMterf4ENSMUSG00000026273
rattus_norvegicusMterf4ENSRNOG00000037376
drosophila_melanogasterCG15390FBGN0031419
caenorhabditis_elegansmter-4WBGENE00010771

Protein

Protein identifiers

Transcription termination factor 4, mitochondrialQ7Z6M4 (reviewed: Q7Z6M4)

Alternative names: Mitochondrial transcription termination factor 4, mTERF domain-containing protein 2

All UniProt accessions (10): B4DFP7, B4DKD5, B5MBW3, C9JNJ7, C9JX74, E7EW93, Q7Z6M4, H7C1N9, H7C316, H7C3Q3

UniProt curated annotations — full annotation on UniProt →

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).

Subunit / interactions. Heterodimer with NSUN4; this interaction may be required for NSUN4 recruitment to the mitochondrial large ribosomal subunit.

Subcellular location. Mitochondrion.

Post-translational modifications. The mature mitochondrial protein exists in 2 forms differing at the level of their N-terminus, one is starting at residue 43 and the other at residue 48.

Domain organisation. The MTERF repeats form a half-donut shaped, right-handed superhelix, where the concave side displays a positively charged path for nucleic acid interaction.

Similarity. Belongs to the mTERF family.

RefSeq proteins (3): NP_001317108, NP_001317109, NP_872307* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003690MTERFFamily
IPR038538MTERF_sfHomologous_superfamily

Pfam: PF02536

UniProt features (42 total): helix 18, sequence variant 5, repeat 5, sequence conflict 4, turn 3, chain 2, region of interest 2, transit peptide 1, compositionally biased region 1, strand 1

Structure

Experimental structures (PDB)

15 structures.

PDBMethodResolution (Å)
4FZVX-RAY DIFFRACTION2
7OF0ELECTRON MICROSCOPY2.2
7OF7ELECTRON MICROSCOPY2.5
7O9MELECTRON MICROSCOPY2.6
7OF3ELECTRON MICROSCOPY2.7
4FP9X-RAY DIFFRACTION2.9
7ODRELECTRON MICROSCOPY2.9
7OF5ELECTRON MICROSCOPY2.9
8QSJELECTRON MICROSCOPY3
8PK0ELECTRON MICROSCOPY3.03
7O9KELECTRON MICROSCOPY3.1
7ODSELECTRON MICROSCOPY3.1
7ODTELECTRON MICROSCOPY3.1
7OICELECTRON MICROSCOPY3.1
7PD3ELECTRON MICROSCOPY3.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q7Z6M4-F177.130.60

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-6793080rRNA modification in the mitochondrion
R-HSA-72312rRNA processing
R-HSA-8868766rRNA processing in the mitochondrion
R-HSA-8953854Metabolism of RNA

MSigDB gene sets: 136 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_RIBOSOME_ASSEMBLY, GOBP_RIBOSOMAL_LARGE_SUBUNIT_ASSEMBLY, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, CCAGGTT_MIR490, GOBP_SENSORY_ORGAN_DEVELOPMENT, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, WANG_RESPONSE_TO_ANDROGEN_UP, GOBP_CIRCULATORY_SYSTEM_DEVELOPMENT, REACTOME_METABOLISM_OF_RNA, OSMAN_BLADDER_CANCER_DN, YAGI_AML_WITH_T_9_11_TRANSLOCATION

GO Biological Process (7): rRNA processing (GO:0006364), heart development (GO:0007507), camera-type eye development (GO:0043010), mitochondrial ribosome assembly (GO:0061668), mitochondrial large ribosomal subunit assembly (GO:1902775), regulation of mitochondrial transcription (GO:1903108), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (7): rRNA binding (GO:0019843), protein-RNA adaptor activity (GO:0140517), RNA folding chaperone (GO:0140691), nucleic acid binding (GO:0003676), double-stranded DNA binding (GO:0003690), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
rRNA processing in the mitochondrion1
Metabolism of RNA1
rRNA processing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cytoplasm2
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
animal organ development1
circulatory system development1
eye development1
ribosome assembly1
ribosomal large subunit assembly1
mitochondrial ribosome assembly1
regulation of DNA-templated transcription1
mitochondrial transcription1
regulation of mitochondrial gene expression1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
RNA binding1
protein-macromolecule adaptor activity1
molecular_function1
RNA folding1
DNA binding1
nucleic acid binding1
intracellular membrane-bounded organelle1
mitochondrion1
intracellular organelle lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

1028 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MTERF4NSUN4Q96CB9998
MTERF4MALSU1Q96EH3829
MTERF4MTG1Q9BT17811
MTERF4MTERF1Q99551771
MTERF4MTERF2Q49AM1769
MTERF4MTG2Q9H4K7739
MTERF4POLRMTO00411731
MTERF4GTPBP10A4D1E9720
MTERF4MRM2Q9UI43708
MTERF4TFB1MQ8WVM0677
MTERF4DDX28Q9NUL7667
MTERF4NSUN3Q9H649663
MTERF4MRM3Q9HC36652
MTERF4MRM1Q6IN84644
MTERF4GTPBP6O43824616

IntAct

54 interactions, top by confidence:

ABTypeScore
MTERF4NSUN4psi-mi:“MI:0915”(physical association)0.760
MTERF4NSUN4psi-mi:“MI:0407”(direct interaction)0.760
KBTBD7METTL15psi-mi:“MI:0914”(association)0.730
CA10WDHD1psi-mi:“MI:0914”(association)0.640
EMDMTERF4psi-mi:“MI:0915”(physical association)0.560
MTERF4BANPpsi-mi:“MI:0915”(physical association)0.560
MTERF4OSGIN1psi-mi:“MI:0915”(physical association)0.560
DGAT2L6MTERF4psi-mi:“MI:0915”(physical association)0.560
MTERF4CIDEBpsi-mi:“MI:0915”(physical association)0.560
MTERF4TNFRSF10Dpsi-mi:“MI:0915”(physical association)0.560
INSL3GAPDHSpsi-mi:“MI:0914”(association)0.530
KBTBD7PLD2psi-mi:“MI:0914”(association)0.530
HDGFL2CDC7psi-mi:“MI:0914”(association)0.530
NDUFAB1MIEF1psi-mi:“MI:0915”(physical association)0.490
HSCBRBP5psi-mi:“MI:0914”(association)0.350
MRPL12psi-mi:“MI:0914”(association)0.350
MND1SPAG9psi-mi:“MI:0914”(association)0.350
KBTBD7GTPBP10psi-mi:“MI:0914”(association)0.350

BioGRID (36): MTERF4 (Affinity Capture-MS), MTERF4 (Affinity Capture-MS), MTERF4 (Affinity Capture-MS), MTERF4 (Affinity Capture-MS), MTERF4 (Affinity Capture-MS), MTERF4 (Affinity Capture-MS), MTERF4 (Affinity Capture-MS), MTERF4 (Affinity Capture-MS), MTERF4 (Affinity Capture-RNA), MTERF4 (Two-hybrid), CIDEB (Two-hybrid), OSGIN1 (Two-hybrid), BANP (Two-hybrid), TNFRSF10D (Two-hybrid), DGAT2L6 (Two-hybrid)

ESM2 similar proteins: A1L3F5, A1L3L1, A2RT67, A6NFN9, A6QPR9, A7MBF6, B9EJ57, F4IHL3, H2LP95, O81916, P0C6R2, Q28CB1, Q29RL0, Q2HJ90, Q49AM1, Q4G078, Q4R683, Q5R6G1, Q5R9U8, Q5RD21, Q5RFI6, Q5XIE2, Q5ZJC8, Q6AUK6, Q6NXY1, Q6P6Q6, Q6ZRR7, Q7L8L6, Q7TMV3, Q7Z494, Q7Z6M4, Q80YS9, Q8BKY8, Q8BVN4, Q8CDN9, Q8CHZ9, Q8NEN0, Q8R3J4, Q8S8F2, Q8W519

Diamond homologs: Q4G078, Q7Z6M4, Q8BVN4

SIGNOR signaling

1 interactions.

AEffectBMechanism
MTERF4“form complex”“MTERF4-NSUN4 mitochondiral ribosomal assembly complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 34 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Mitochondrial ribosome-associated quality control526.7×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

273 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance209
Likely benign18
Benign4

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
830538NC_000002.11:g.(?241808273)(242708241_?)delPathogenic

SpliceAI

2700 predictions. Top by Δscore:

VariantEffectΔscore
2:241073361:GGAA:Gdonor_gain1.0000
2:241073362:G:GTdonor_gain1.0000
2:241073362:GAA:Gdonor_gain1.0000
2:241073365:G:GGdonor_gain1.0000
2:241096439:C:CCacceptor_gain1.0000
2:241097239:TCA:Tdonor_loss1.0000
2:241097240:CA:Cdonor_loss1.0000
2:241097241:ACCTG:Adonor_loss1.0000
2:241097242:CCTG:Cdonor_loss1.0000
2:241102248:CTTA:Cdonor_loss1.0000
2:241102249:TTACC:Tdonor_loss1.0000
2:241102250:TACCT:Tdonor_loss1.0000
2:241081676:GAC:Gacceptor_gain0.9900
2:241081789:GCTCG:Gdonor_gain0.9900
2:241081790:CTCGG:Cdonor_loss0.9900
2:241081791:TCGGT:Tdonor_loss0.9900
2:241081792:CGG:Cdonor_loss0.9900
2:241081793:GGT:Gdonor_loss0.9900
2:241081794:GT:Gdonor_loss0.9900
2:241081795:TAAGT:Tdonor_loss0.9900
2:241094275:ACCT:Adonor_gain0.9900
2:241094276:CCTC:Cdonor_gain0.9900
2:241094278:T:TAdonor_gain0.9900
2:241094343:A:Cdonor_gain0.9900
2:241094430:CTG:Cacceptor_gain0.9900
2:241095953:T:Adonor_gain0.9900
2:241095954:C:Adonor_gain0.9900
2:241095988:T:TAdonor_gain0.9900
2:241096002:T:TAdonor_gain0.9900
2:241096005:T:TAdonor_gain0.9900

AlphaMissense

2540 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:241096241:A:CF301L0.993
2:241096241:A:TF301L0.993
2:241096243:A:GF301L0.993
2:241096335:C:GR270P0.992
2:241096427:G:CF239L0.991
2:241096427:G:TF239L0.991
2:241096429:A:GF239L0.991
2:241097246:A:CF234L0.991
2:241097246:A:TF234L0.991
2:241097248:A:GF234L0.991
2:241096196:A:CF316L0.990
2:241096196:A:TF316L0.990
2:241096198:A:GF316L0.990
2:241096242:A:GF301S0.989
2:241096324:A:CY274D0.989
2:241097328:A:GF207S0.989
2:241096188:A:GL319P0.985
2:241096341:A:GL268P0.985
2:241097247:A:GF234S0.984
2:241096352:T:AR264S0.982
2:241096352:T:GR264S0.982
2:241097327:G:CF207L0.982
2:241097327:G:TF207L0.982
2:241097329:A:GF207L0.982
2:241097335:A:GC205R0.982
2:241096323:T:GY274S0.981
2:241099605:A:GF104S0.981
2:241096242:A:CF301C0.979
2:241096345:A:CY267D0.978
2:241096336:G:TR270S0.977

dbSNP variants (sampled 300 via entrez): RS1000015077 (2:241076422 G>T), RS1000107414 (2:241090887 A>G), RS1000196783 (2:241075563 C>A), RS1000210579 (2:241061884 A>G), RS1000217825 (2:241045038 G>A), RS1000242987 (2:241081677 A>G,T), RS1000340659 (2:241087751 G>A), RS1000352817 (2:241070666 G>A), RS1000372052 (2:241087521 C>G), RS1000440430 (2:241044787 C>G), RS1000453581 (2:241065972 G>C), RS1000492617 (2:241071384 C>T), RS1000506931 (2:241056875 C>T), RS1000531170 (2:241074369 C>T), RS1000572298 (2:241081838 G>A)

Disease associations

OMIM: gene MIM:615393 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST001554_3Sex hormone-binding globulin levels3.000000e-06
GCST012227_981Hip circumference adjusted for BMI8.000000e-11

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004696sex hormone-binding globulin measurement
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases expression, increases methylation2
Acetaminophendecreases expression, increases expression2
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
sodium arsenitedecreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
di-n-butylphosphoric acidaffects expression1
Zoledronic Acidincreases expression1
Vorinostatincreases expression1
Leflunomideincreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation1
Benzo(a)pyrenedecreases expression1
Doxorubicindecreases expression1
Colforsindecreases expression1
Ozoneaffects cotreatment, increases oxidation, increases abundance1
Ribonucleotidesaffects binding1
Tretinoindecreases expression1
Valproic Aciddecreases expression1
1-Methyl-4-phenylpyridiniumincreases cleavage, decreases expression, decreases reaction1
Metriboloneincreases expression1
Antirheumatic Agentsincreases expression1
Cadmium Chloridedecreases expression1
Okadaic Aciddecreases expression1
Volatile Organic Compoundsaffects cotreatment, increases oxidation1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_KT78HeLa SilenciX MTERFD2Cancer cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.