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METTL17

gene
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Also known as FLJ20859

Summary

METTL17 (methyltransferase like 17, HGNC:19280) is a protein-coding gene on chromosome 14q11.2, encoding Ribosome assembly protein METTL17, mitochondrial (Q9H7H0). Mitochondrial ribosome (mitoribosome) assembly factor. It is a selective cancer dependency (DepMap: 51.2% of cell lines).

Enables 4 iron, 4 sulfur cluster binding activity. Involved in mitochondrial small ribosomal subunit assembly. Located in nucleoplasm.

Source: NCBI Gene 64745 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 59 total
  • Cancer dependency (DepMap): dependent in 51.2% of screened cell lines
  • MANE Select transcript: NM_022734

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19280
Approved symbolMETTL17
Namemethyltransferase like 17
Location14q11.2
Locus typegene with protein product
StatusApproved
AliasesFLJ20859
Ensembl geneENSG00000165792
Ensembl biotypeprotein_coding
OMIM616091
Entrez64745

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 12 retained_intron, 11 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000339374, ENST00000382985, ENST00000553389, ENST00000553441, ENST00000553536, ENST00000553564, ENST00000554283, ENST00000554354, ENST00000554588, ENST00000554751, ENST00000554849, ENST00000554949, ENST00000554985, ENST00000555177, ENST00000555390, ENST00000555533, ENST00000555640, ENST00000555670, ENST00000555902, ENST00000556442, ENST00000556670, ENST00000556733, ENST00000557279, ENST00000557550, ENST00000557701, ENST00000908545, ENST00000908546, ENST00000967486

RefSeq mRNA: 2 — MANE Select: NM_022734 NM_001029991, NM_022734

CCDS: CCDS41913, CCDS9562

Canonical transcript exons

ENST00000339374 — 14 exons

ExonStartEnd
ENSE000034837152099590120995951
ENSE000034839292099678520997035
ENSE000035030632099254120992622
ENSE000035198742098998020990077
ENSE000035221602099396920994063
ENSE000035249552099046420990598
ENSE000035655712099311820993191
ENSE000036010692099652720996711
ENSE000036084112099479420994901
ENSE000036161892099023020990383
ENSE000036638842099620920996292
ENSE000036691922099516520995233
ENSE000036758872099212420992205
ENSE000037885632099454320994613

Expression profiles

Bgee: expression breadth ubiquitous, 269 present calls, max score 98.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.2430 / max 141.7376, expressed in 1815 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
13849129.24301815

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right adrenal gland cortexUBERON:003582798.37gold quality
right adrenal glandUBERON:000123398.22gold quality
right uterine tubeUBERON:000130297.87gold quality
left adrenal glandUBERON:000123497.79gold quality
left adrenal gland cortexUBERON:003582597.77gold quality
metanephros cortexUBERON:001053397.76gold quality
right hemisphere of cerebellumUBERON:001489097.48gold quality
small intestine Peyer’s patchUBERON:000345497.46gold quality
adrenal cortexUBERON:000123597.44gold quality
cerebellar hemisphereUBERON:000224597.44gold quality
cerebellar cortexUBERON:000212997.38gold quality
tibial nerveUBERON:000132397.31gold quality
body of uterusUBERON:000985397.25gold quality
mucosa of transverse colonUBERON:000499197.18gold quality
transverse colonUBERON:000115797.17gold quality
body of pancreasUBERON:000115097.15gold quality
endocervixUBERON:000045897.12gold quality
left lobe of thyroid glandUBERON:000112097.07gold quality
left ovaryUBERON:000211997.04gold quality
right ovaryUBERON:000211897.03gold quality
adrenal glandUBERON:000236997.01gold quality
ectocervixUBERON:001224996.99gold quality
right lobe of thyroid glandUBERON:000111996.94gold quality
apex of heartUBERON:000209896.93gold quality
muscle layer of sigmoid colonUBERON:003580596.87gold quality
secondary oocyteCL:000065596.84gold quality
skin of legUBERON:000151196.82gold quality
skin of abdomenUBERON:000141696.75gold quality
minor salivary glandUBERON:000183096.75gold quality
body of stomachUBERON:000116196.63gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting METTL17, 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-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-428299.9975.366408
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-216A-5P99.5068.021288
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-371A-5P99.0866.511914
HSA-MIR-4477A98.8369.752952
HSA-MIR-6826-3P98.1966.321153
HSA-MIR-63497.7467.11818
HSA-MIR-3622A-5P97.4367.11356

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 51.2% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 5)

  • Possible component of the small subunit of the mitochondrial ribosome, has similarity to yeast Rsm22 (Ykl155c) mitochondrial ribosomal protein. (PMID:11278769)
  • METT11D1 mutations could not explain phenotype of patients with combined oxidative phosphorylation system deficiencies. (PMID:24137763)
  • METTL17 is a novel coactivator of estrogen receptors and may play a role in breast tumorigenesis. (PMID:26488768)
  • efects of mitochondrial ribosome caused by deletion of Mettl17 lead to the impaired translation of mitochondrial protein-coding genes, resulting in significant changes in mitochondrial oxidative phosphorylation and cellular metabolome, which are important for mESC pluripotency (PMID:31487196)
  • METTL17 coordinates ferroptosis and tumorigenesis by regulating mitochondrial translation in colorectal cancer. (PMID:38377789)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriomettl17ENSDARG00000103889
mus_musculusMettl17ENSMUSG00000004561
rattus_norvegicusMettl17ENSRNOG00000025512
drosophila_melanogasterCG13126FBGN0032168

Paralogs (1): COX11 (ENSG00000166260)

Protein

Protein identifiers

Ribosome assembly protein METTL17, mitochondrial — Q9H7H0 (reviewed: Q9H7H0)

Alternative names: False p73 target gene protein, Methyltransferase 11 domain-containing protein 1, Methyltransferase-like protein 17, Protein RSM22 homolog, mitochondrial

All UniProt accessions (9): A0A0S2Z5L8, A0A0S2Z5V5, B4E298, Q9H7H0, G3V353, G3V3X6, G3V4H5, G3V4P2, H0YJW1

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial ribosome (mitoribosome) assembly factor. Binds at the interface of the head and body domains of the mitochondrial small ribosomal subunit (mt-SSU), occluding the mRNA channel and preventing compaction of the head domain towards the body. Probable inactive methyltransferase: retains the characteristic folding and ability to bind S-adenosyl-L-methionine, but it probably lost its methyltransferase activity.

Subunit / interactions. Associates with the mitochondrial ribosome (mitoribosome).

Subcellular location. Mitochondrion matrix.

Domain organisation. [4Fe-4S] cluster-binding is essential for its ability to promote assembly of the mitochondrial ribosome (mitoribosome).

Similarity. Belongs to the methyltransferase superfamily. Rsm22 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9H7H0-11yes
Q9H7H0-22
Q9H7H0-33

RefSeq proteins (2): NP_001025162, NP_073571* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR015324Ribosomal_Rsm22-likeFamily
IPR029063SAM-dependent_MTases_sfHomologous_superfamily
IPR052571Mt_RNA_MethyltransferaseFamily

Pfam: PF09243

UniProt features (57 total): strand 20, helix 14, mutagenesis site 5, turn 5, binding site 4, sequence variant 3, sequence conflict 2, splice variant 2, transit peptide 1, chain 1

Structure

Experimental structures (PDB)

6 structures.

PDBMethodResolution (Å)
8CSSELECTRON MICROSCOPY2.36
8CSQELECTRON MICROSCOPY2.54
8CSRELECTRON MICROSCOPY2.54
8CSPELECTRON MICROSCOPY2.66
8CSTELECTRON MICROSCOPY2.85
8CSUELECTRON MICROSCOPY3.03

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H7H0-F186.260.71

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (4): 333; 339; 347; 404

Mutagenesis-validated functional residues (5):

PositionPhenotype
333abolished iron-sulfur-binding, leading to impaired ability to promote mitochondrial ribosome assembly; when associated w
339abolished iron-sulfur-binding, leading to impaired ability to promote mitochondrial ribosome assembly; when associated w
347abolished iron-sulfur-binding, leading to impaired ability to promote mitochondrial ribosome assembly; when associated w
404abolished iron-sulfur-binding, leading to impaired ability to promote mitochondrial ribosome assembly; when associated w
424–426impaired ability to promote mitochondrial ribosome assembly.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 117 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, GOBP_RIBOSOME_BIOGENESIS, TAATAAT_MIR126, GCM_GSPT1, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_RIBOSOME_ASSEMBLY, GOBP_TRANSLATION, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, GCM_NUMA1, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GCM_NF2, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS

GO Biological Process (4): translation (GO:0006412), ribosomal small subunit biogenesis (GO:0042274), mitochondrial small ribosomal subunit assembly (GO:0180026), methylation (GO:0032259)

GO Molecular Function (9): metal ion binding (GO:0046872), 4 iron, 4 sulfur cluster binding (GO:0051539), mitochondrial ribosome binding (GO:0097177), S-adenosyl-L-methionine binding (GO:1904047), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740), small molecule binding (GO:0036094), iron-sulfur cluster binding (GO:0051536)

GO Cellular Component (4): nucleoplasm (GO:0005654), mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), intracellular organelle lumen (GO:0070013)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cation binding2
binding2
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
ribonucleoprotein complex biogenesis1
ribosome biogenesis1
ribosomal small subunit assembly1
mitochondrial ribosome assembly1
metabolic process1
iron-sulfur cluster binding1
ribosome binding1
sulfur compound binding1
transferase activity, transferring one-carbon groups1
catalytic activity1
metal cluster binding1
nuclear lumen1
cellular anatomical structure1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrion1
intracellular organelle lumen1
intracellular organelle1
organelle lumen1

Protein interactions and networks

STRING

1508 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
METTL17NTMT1Q9BV86606
METTL17METTL27Q8N6F8584
METTL17METTL15A6NJ78581
METTL17METTL5Q9NRN9578
METTL17METTL18O95568557
METTL17METTL9Q9H1A3532
METTL17NTMT2Q5VVY1526
METTL17CHCHD1Q96BP2519
METTL17METTL25Q8N6Q8505
METTL17TMT1AQ9H8H3497
METTL17TMEM126AQ9H061488
METTL17ESR2Q92731483
METTL17METTL26Q96S19480
METTL17TRUB2O95900472
METTL17METTL1Q9UBP6455
METTL17RPUSD3Q6P087455

IntAct

164 interactions, top by confidence:

ABTypeScore
METTL17TRAF1psi-mi:“MI:0915”(physical association)0.780
METTL17CALCOCO2psi-mi:“MI:0915”(physical association)0.780
METTL17PNMA1psi-mi:“MI:0915”(physical association)0.780
METTL17CEP70psi-mi:“MI:0915”(physical association)0.780
TRAF1METTL17psi-mi:“MI:0915”(physical association)0.780
CALCOCO2METTL17psi-mi:“MI:0915”(physical association)0.780
PNMA1METTL17psi-mi:“MI:0915”(physical association)0.780
CEP70METTL17psi-mi:“MI:0915”(physical association)0.780
TRIP6METTL17psi-mi:“MI:0915”(physical association)0.740
METTL17TFIP11psi-mi:“MI:0915”(physical association)0.740

BioGRID (470): METTL17 (Two-hybrid), METTL17 (Two-hybrid), METTL17 (Two-hybrid), METTL17 (Two-hybrid), METTL17 (Two-hybrid), METTL17 (Two-hybrid), METTL17 (Two-hybrid), CEP70 (Two-hybrid), KRT40 (Two-hybrid), SPERT (Two-hybrid), METTL17 (Affinity Capture-MS), METTL17 (Two-hybrid), METTL17 (Two-hybrid), TRIP6 (Two-hybrid), METTL17 (Affinity Capture-MS)

ESM2 similar proteins: A0PJW6, A5PJW2, B3DI94, B5DFG1, O00411, O95382, P49753, Q059A4, Q0V9C9, Q3SX05, Q4KLZ1, Q4KM93, Q4R5Q4, Q4VAE3, Q53S58, Q5EA71, Q5T1A1, Q5XIC2, Q643R3, Q66LN0, Q6DC58, Q6NVG1, Q76MJ5, Q7YS91, Q80YU0, Q863F8, Q8BPE4, Q8BWM0, Q8N159, Q8NFF5, Q8VCA6, Q8VD26, Q921N7, Q96AN5, Q96KR6, Q99MQ3, Q9BQ95, Q9BUB7, Q9BYK8, Q9CQE2

Diamond homologs: Q2TBP8, Q3U2U7, Q9H7H0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 123 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 translation1727.9×1e-18
Mitochondrial translation initiation1827.2×3e-19
Mitochondrial translation elongation1827.2×3e-19
Mitochondrial ribosome-associated quality control1826.3×3e-19
Mitochondrial translation termination1823.5×1e-18
SARS-CoV-1 modulates host translation machinery622.1×4e-06
Eukaryotic Translation Initiation518.4×9e-05
Cap-dependent Translation Initiation518.4×9e-05

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation1827.4×1e-18
cytoplasmic translation914.6×2e-06
translation1614.4×5e-12
ribosomal small subunit biogenesis612.0×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance36
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1363 predictions. Top by Δscore:

VariantEffectΔscore
14:20990384:G:GAdonor_loss1.0000
14:20990385:T:Adonor_loss1.0000
14:20990386:GAG:Gdonor_loss1.0000
14:20990387:AGTAA:Adonor_loss1.0000
14:20992123:GACTT:Gacceptor_gain1.0000
14:20992204:AG:Adonor_loss1.0000
14:20992206:G:GCdonor_loss1.0000
14:20992206:G:GGdonor_gain1.0000
14:20992207:T:Adonor_loss1.0000
14:20993964:CTTA:Cacceptor_loss1.0000
14:20993965:TTAG:Tacceptor_loss1.0000
14:20993966:TA:Tacceptor_loss1.0000
14:20993967:A:AGacceptor_gain1.0000
14:20993968:G:GGacceptor_gain1.0000
14:20994061:AAGG:Adonor_loss1.0000
14:20994062:AGGT:Adonor_loss1.0000
14:20994064:GT:Gdonor_loss1.0000
14:20994065:T:Gdonor_loss1.0000
14:20995156:T:TAacceptor_gain1.0000
14:20995158:T:TAacceptor_gain1.0000
14:20995159:GAACA:Gacceptor_loss1.0000
14:20995162:CAGGT:Cacceptor_loss1.0000
14:20995163:A:AGacceptor_gain1.0000
14:20995163:A:ATacceptor_loss1.0000
14:20995164:G:GGacceptor_gain1.0000
14:20995232:AGGT:Adonor_loss1.0000
14:20995233:GGTAA:Gdonor_loss1.0000
14:20995234:G:GAdonor_loss1.0000
14:20995234:G:GGdonor_gain1.0000
14:20995892:T:TAacceptor_gain1.0000

AlphaMissense

2935 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
14:20996802:C:AA428D0.985
14:20996209:T:CC333R0.984
14:20993160:G:CD191H0.983
14:20996810:A:CS431R0.983
14:20996812:C:AS431R0.983
14:20996812:C:GS431R0.983
14:20993190:T:AW201R0.982
14:20993190:T:CW201R0.982
14:20996227:T:CC339R0.980
14:20996551:T:CF369L0.979
14:20996553:C:AF369L0.979
14:20996553:C:GF369L0.979
14:20996647:T:CC401R0.976
14:20996552:T:CF369S0.975
14:20995175:A:TE296V0.974
14:20996605:C:AR387S0.974
14:20996792:T:GY425D0.970
14:20995218:G:CR310S0.969
14:20995218:G:TR310S0.969
14:20994878:T:AW285R0.968
14:20994878:T:CW285R0.968
14:20992557:A:CS155R0.967
14:20992559:C:AS155R0.967
14:20992559:C:GS155R0.967
14:20996227:T:AC339S0.967
14:20996228:G:CC339S0.967
14:20996656:T:CC404R0.967
14:20993985:T:AW207R0.966
14:20993985:T:CW207R0.966
14:20994055:T:CL230P0.965

dbSNP variants (sampled 300 via entrez): RS1000185701 (14:20992853 C>A,G), RS1000317830 (14:20993781 CTT>C,CT,CTTT,CTTTT,CTTTTT), RS1000544424 (14:20988754 C>G,T), RS1000662131 (14:20992437 G>A), RS1001307849 (14:20988179 A>T), RS1001319531 (14:20993650 T>G), RS1001515347 (14:20990173 G>A,T), RS1001961943 (14:20989588 T>A), RS1002218070 (14:20993625 C>T), RS1002666507 (14:20990284 C>G,T), RS1002727902 (14:20994726 T>C), RS1003316933 (14:20996067 A>G), RS1003594719 (14:20992034 G>A,C,T), RS1003610356 (14:20996374 G>A,C,T), RS1004050091 (14:20990932 G>GT)

Disease associations

OMIM: gene MIM:616091 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST009304_1Degraded stimulus continuous performance test score7.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007636attention function measurement

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
sodium arsenitedecreases expression, increases abundance2
Air Pollutantsdecreases expression, affects cotreatment, increases abundance, increases oxidation2
alpha-pineneincreases abundance, affects cotreatment, increases oxidation1
bisphenol Adecreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
K 7174decreases expression1
Decitabineaffects expression1
Acetaminophendecreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Arsenicdecreases expression, increases abundance1
Cadmiumincreases abundance, increases expression1
Cisplatinaffects expression1
Doxorubicindecreases expression1
Ozoneaffects cotreatment, increases oxidation, increases abundance1
Ribonucleotidesaffects binding1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1increases methylation1
Sodium Selenitedecreases expression1
Antirheumatic Agentsincreases expression1
Cadmium Chlorideincreases abundance, increases expression1
Particulate Matterdecreases expression, increases abundance1
Volatile Organic Compoundsaffects cotreatment, increases oxidation1

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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot