METTL5

gene
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Also known as HSPC133

Summary

METTL5 (methyltransferase 5, N6-adenosine, HGNC:25006) is a protein-coding gene on chromosome 2q31.1, encoding rRNA N(6)-adenosine-methyltransferase METTL5 (Q9NRN9). Catalytic subunit of a heterodimer with TRMT112, which specifically methylates the 6th position of adenine in position 1832 of 18S rRNA.

Enables S-adenosyl-L-methionine binding activity and rRNA (adenine-N6-)-methyltransferase activity. Involved in positive regulation of translation and rRNA methylation. Located in several cellular components, including fibrillar center; postsynapse; and presynapse. Implicated in autosomal recessive intellectual developmental disorder 72.

Source: NCBI Gene 29081 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): intellectual developmental disorder, autosomal recessive 72 (Strong, GenCC) — +1 more curated relationship
  • GWAS associations: 1
  • Clinical variants (ClinVar): 70 total — 4 pathogenic, 3 likely-pathogenic
  • Phenotypes (HPO): 17
  • Druggable target: yes
  • MANE Select transcript: NM_014168

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25006
Approved symbolMETTL5
Namemethyltransferase 5, N6-adenosine
Location2q31.1
Locus typegene with protein product
StatusApproved
AliasesHSPC133
Ensembl geneENSG00000138382
Ensembl biotypeprotein_coding
OMIM618628
Entrez29081

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 13 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000260953, ENST00000308099, ENST00000392640, ENST00000409340, ENST00000409837, ENST00000409965, ENST00000410097, ENST00000442181, ENST00000471560, ENST00000484351, ENST00000537825, ENST00000538491, ENST00000938651, ENST00000938652, ENST00000938653, ENST00000938654

RefSeq mRNA: 3 — MANE Select: NM_014168 NM_001293186, NM_001293187, NM_014168

CCDS: CCDS33320

Canonical transcript exons

ENST00000260953 — 7 exons

ExonStartEnd
ENSE00000882688169821943169822057
ENSE00001129808169821092169821273
ENSE00001466639169824489169824905
ENSE00001580434169811757169811858
ENSE00003510429169812457169812506
ENSE00003668398169815477169815528
ENSE00003687414169819561169819643

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 97.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.4120 / max 620.4743, expressed in 1814 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
3174232.23491811
317411.0472631
2024650.129941

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183197.37gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450297.37gold quality
biceps brachiiUBERON:000150797.33gold quality
calcaneal tendonUBERON:000370197.20gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451197.09gold quality
vastus lateralisUBERON:000137996.95gold quality
islet of LangerhansUBERON:000000696.81gold quality
quadriceps femorisUBERON:000137796.81gold quality
heart right ventricleUBERON:000208096.78gold quality
palpebral conjunctivaUBERON:000181296.56gold quality
tendonUBERON:000004396.55gold quality
left coronary arteryUBERON:000162696.53gold quality
right coronary arteryUBERON:000162596.47gold quality
skin of hipUBERON:000155496.33gold quality
coronary arteryUBERON:000162196.25gold quality
hindlimb stylopod muscleUBERON:000425296.25gold quality
buccal mucosa cellCL:000233696.24gold quality
ascending aortaUBERON:000149696.21gold quality
thoracic aortaUBERON:000151596.20gold quality
tibial arteryUBERON:000761096.20gold quality
aortaUBERON:000094796.19gold quality
arteryUBERON:000163796.19gold quality
popliteal arteryUBERON:000225096.19gold quality
renal glomerulusUBERON:000007496.18gold quality
descending thoracic aortaUBERON:000234596.07gold quality
body of tongueUBERON:001187696.01gold quality
deltoidUBERON:000147695.96gold quality
metanephric glomerulusUBERON:000473695.96gold quality
lower esophagusUBERON:001347395.74gold quality
lower esophagus muscularis layerUBERON:003583395.74gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-112yes6.84
E-MTAB-6379no901.73
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 12)

  • METTL5-TRMT112 partners act by extruding the adenosine to be modified from a double-stranded nucleic acid. (PMID:31328227)
  • Ribosome 18S m(6)A Methyltransferase METTL5 Promotes Translation Initiation and Breast Cancer Cell Growth. (PMID:33357433)
  • Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima. (PMID:33428944)
  • Analysis of the role of METTL5 as a hub gene in lung adenocarcinoma based on a weighted gene co-expression network. (PMID:34517547)
  • The potential role of methyltransferase-like 5 in deficient mismatch repair of uterine corpus endometrial carcinoma. (PMID:35166644)
  • Three Afghani siblings with a novel homozygous variant and further delineation of the clinical features of METTL5 related intellectual disability syndrome. (PMID:36305450)
  • Knockdown of METTL5 inhibits the Myc pathway to downregulate PD-L1 expression and inhibits immune escape of hepatocellular carcinoma cells. (PMID:36369791)
  • METTL5 stabilizes c-Myc by facilitating USP5 translation to reprogram glucose metabolism and promote hepatocellular carcinoma progression. (PMID:36602428)
  • The m6A methyltransferase METTL5 promotes neutrophil extracellular trap network release to regulate hepatocellular carcinoma progression. (PMID:38613157)
  • Biological significance of METTL5 in atherosclerosis: comprehensive analysis of single-cell and bulk RNA sequencing data. (PMID:38663914)
  • METTL5: A Potential Biomarker for Nonsmall Cell Lung Cancer That Promotes Cancer Cell Proliferation by Interacting with IGF2BP3. (PMID:39023781)
  • METTL5 enhances the mRNA stability of TPRKB through m[6]A modification to facilitate the aggressive phenotypes of hepatocellular carcinoma cell. (PMID:39182664)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomettl5ENSDARG00000068893
mus_musculusMettl5ENSMUSG00000051730
rattus_norvegicusMettl5ENSRNOG00000008469
drosophila_melanogasterMettl5FBGN0036856
caenorhabditis_elegansWBGENE00008008

Protein

Protein identifiers

rRNA N(6)-adenosine-methyltransferase METTL5Q9NRN9 (reviewed: Q9NRN9)

Alternative names: Methyltransferase-like protein 5

All UniProt accessions (8): B8ZZC8, B8ZZE3, B8ZZY8, E7EMN2, Q9NRN9, F5H4E8, H0YFV5, H7C0M7

UniProt curated annotations — full annotation on UniProt →

Function. Catalytic subunit of a heterodimer with TRMT112, which specifically methylates the 6th position of adenine in position 1832 of 18S rRNA. N6-methylation of adenine(1832) in 18S rRNA resides in the decoding center of 18S rRNA and is required for translation and embryonic stem cells (ESCs) pluripotency and differentiation.

Subunit / interactions. Heterodimer; heterodimerizes with TRMT112.

Subcellular location. Nucleus. Presynapse. Postsynapse.

Tissue specificity. Expressed from very early development (8 post-conceptual weeks) and expression persists through adulthood in multiple substructures of the brain, including the cerebellar cortex, hippocampus, and striatum.

Disease relevance. Intellectual developmental disorder, autosomal recessive 72 (MRT72) [MIM:618665] A form of intellectual disability, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT72 patients manifest moderate to severe intellectual disability, microcephaly, and dysmorphic facial features. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. rRNA N6-adenosine-methyltransferase activity is inhibited by zinc.

Similarity. Belongs to the methyltransferase superfamily. PrmA family.

RefSeq proteins (3): NP_001280115, NP_001280116, NP_054887* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002052DNA_methylase_N6_adenine_CSConserved_site
IPR007848Small_mtfrase_domDomain
IPR029063SAM-dependent_MTases_sfHomologous_superfamily
IPR051720rRNA_MeTrfase/Polyamine_SynthFamily

Pfam: PF05175

Catalyzed reactions (Rhea), 1 shown:

  • adenosine(1832) in 18S rRNA + S-adenosyl-L-methionine = N(6)-methyladenosine(1832) in 18S rRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:62612)

UniProt features (29 total): helix 8, strand 8, binding site 7, sequence variant 2, chain 1, mutagenesis site 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
9OHLX-RAY DIFFRACTION1.29
6H2UX-RAY DIFFRACTION1.6
6H2VX-RAY DIFFRACTION2.49

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NRN9-F192.360.80

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 (7): 28; 31; 59; 62; 64; 81; 108–109

Mutagenesis-validated functional residues (1):

PositionPhenotype
126–128in mettl5-3a; abolished methyltransferase activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 211 (showing top): GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_RNA_METHYLATION, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_RNA_MODIFICATION, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_STEM_CELL_DIFFERENTIATION, ACEVEDO_LIVER_CANCER_UP, GOBP_RRNA_MODIFICATION, GOBP_METHYLATION, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GNF2_HAT1, GOBP_RRNA_METHYLATION, GRADE_COLON_AND_RECTAL_CANCER_UP

GO Biological Process (5): rRNA processing (GO:0006364), rRNA methylation (GO:0031167), positive regulation of translation (GO:0045727), stem cell differentiation (GO:0048863), methylation (GO:0032259)

GO Molecular Function (7): nucleic acid binding (GO:0003676), rRNA (adenine-N6-)-methyltransferase activity (GO:0008988), S-adenosyl-L-methionine binding (GO:1904047), protein binding (GO:0005515), methyltransferase activity (GO:0008168), S-adenosylmethionine-dependent methyltransferase activity (GO:0008757), transferase activity (GO:0016740)

GO Cellular Component (8): fibrillar center (GO:0001650), nucleus (GO:0005634), nucleolus (GO:0005730), cytosol (GO:0005829), presynapse (GO:0098793), postsynapse (GO:0098794), cell projection (GO:0042995), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
binding2
synapse2
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
rRNA modification1
RNA methylation1
translation1
regulation of translation1
positive regulation of gene expression1
positive regulation of protein metabolic process1
cell differentiation1
metabolic process1
N-methyltransferase activity1
rRNA (adenine) methyltransferase activity1
cation binding1
sulfur compound binding1
transferase activity, transferring one-carbon groups1
methyltransferase activity1
catalytic activity1
nucleolus1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular membraneless organelle1
cytoplasm1
cell junction1

Protein interactions and networks

STRING

1134 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
METTL5TRMT112Q9UI30996
METTL5ZCCHC4Q9H5U6969
METTL5METTL16Q86W50951
METTL5ZC3H13Q5T200924
METTL5VIRMAQ69YN4895
METTL5WTAPQ15007815
METTL5METTL3Q86U44812
METTL5RBM15Q96T37784
METTL5METTL14Q9HCE5709
METTL5CBLL1Q75N03670
METTL5METTL15A6NJ78644
METTL5TYW2Q53H54641
METTL5BUD23O43709624
METTL5METTL4Q8N3J2612
METTL5HEMK2Q9Y5N5598

IntAct

13 interactions, top by confidence:

ABTypeScore
TRMT112BUD23psi-mi:“MI:0914”(association)0.910
METTL5TRMT112psi-mi:“MI:0915”(physical association)0.710
METTL5TRMT112psi-mi:“MI:0403”(colocalization)0.710
ZBTB5METTL5psi-mi:“MI:0915”(physical association)0.560
NTF3HSPA5psi-mi:“MI:0914”(association)0.350
METTL5ZBTB5psi-mi:“MI:0915”(physical association)0.000
METTL5TRMT112psi-mi:“MI:0915”(physical association)0.000

BioGRID (19): METTL5 (Co-fractionation), METTL5 (Affinity Capture-MS), ZBTB5 (Two-hybrid), TRMT112 (Two-hybrid), METTL5 (Affinity Capture-MS), USP5 (Affinity Capture-MS), FBXW7 (Affinity Capture-MS), FBXO32 (Affinity Capture-MS), SKP2 (Affinity Capture-MS), USP7 (Affinity Capture-MS), USP37 (Affinity Capture-MS), USP28 (Affinity Capture-MS), USP36 (Affinity Capture-MS), TRIM32 (Affinity Capture-MS), METTL5 (Proximity Label-MS)

ESM2 similar proteins: A6TRI3, A7N1I9, A7SE07, A7Z7T3, A8H551, A9KLV5, B0TSA1, B1HXA1, B4S0J8, B5FAT6, B5FE19, B6EGJ0, B6ELD3, B8F3G3, F1QVR8, O07635, O34522, P39199, P53384, P67502, P67503, Q03432, Q0SQX5, Q0TNA4, Q0WDE1, Q15TV2, Q18511, Q1WUP5, Q2FXG9, Q32DK7, Q3K307, Q3KQF0, Q5E3U5, Q5E5B4, Q5E7A8, Q5EB25, Q5I050, Q65G12, Q7MJ72, Q7MKX1

Diamond homologs: A0KNJ1, A0Q1R2, A1AGF9, A1KS36, A4WF74, A5I638, A5UD93, A5UIB7, A6LRN8, A6TES6, A7FDQ3, A7FXL3, A7GHH4, A7MXI3, A7ZSF3, A8A570, A8AQF7, A8GK75, A9MNA2, B0K3X8, B0KA79, B1ILM1, B1IQ33, B1JKF2, B1KZN5, B1LGM4, B1XHM8, B1XKZ0, B2K467, B2TM01, B2U2N5, B2V2I9, B2VL75, B3PBH5, B4EX23, B4SUN8, B4TJV7, B4TX91, B5BGT7, B5F7P3

SIGNOR signaling

1 interactions.

AEffectBMechanism
METTL5“form complex”“METTL5-TRM112 methyltransferase complex”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic3
Uncertain significance38
Likely benign1
Benign2

Top pathogenic / likely-pathogenic (7)

Variant IDHGVSClassification
1685946NM_014168.4(METTL5):c.591+2T>GPathogenic
3064180NM_014168.4(METTL5):c.224+1G>APathogenic
3391100NM_014168.4(METTL5):c.542-1G>TPathogenic
689379NM_014168.4(METTL5):c.344_345del (p.Arg115fs)Pathogenic
1804912NM_014168.4(METTL5):c.406+1_406+2insATACAAATTCLikely pathogenic
3065390NM_014168.4(METTL5):c.225-1G>TLikely pathogenic
3393292NM_014168.4(METTL5):c.196dup (p.Ser66fs)Likely pathogenic

SpliceAI

1338 predictions. Top by Δscore:

VariantEffectΔscore
2:169810281:A:AGacceptor_gain1.0000
2:169810282:G:GGacceptor_gain1.0000
2:169810282:GA:Gacceptor_gain1.0000
2:169810282:GAA:Gacceptor_gain1.0000
2:169810850:T:TAacceptor_gain1.0000
2:169810855:TA:Tacceptor_loss1.0000
2:169810856:AGG:Aacceptor_gain1.0000
2:169810857:G:GGacceptor_loss1.0000
2:169810857:GGG:Gacceptor_gain1.0000
2:169811034:G:GTdonor_gain1.0000
2:169811034:G:Tdonor_gain1.0000
2:169811038:TCAAA:Tdonor_gain1.0000
2:169811180:CAGGT:Cacceptor_loss1.0000
2:169811181:A:ACacceptor_loss1.0000
2:169811182:G:Aacceptor_loss1.0000
2:169811324:G:Tdonor_loss1.0000
2:169811325:T:Adonor_loss1.0000
2:169812455:A:ACdonor_gain1.0000
2:169812456:C:CCdonor_gain1.0000
2:169819554:AACTT:Adonor_loss1.0000
2:169819555:ACTT:Adonor_loss1.0000
2:169819556:CTTA:Cdonor_loss1.0000
2:169819557:TT:Tdonor_loss1.0000
2:169819558:TAC:Tdonor_loss1.0000
2:169819559:A:ACdonor_gain1.0000
2:169819559:A:Cdonor_loss1.0000
2:169819560:C:CTdonor_gain1.0000
2:169819560:CTT:Cdonor_gain1.0000
2:169819560:CTTCT:Cdonor_gain1.0000
2:169821939:GTAC:Gdonor_loss1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000062870 (2:169812221 T>C), RS1000117530 (2:169818871 C>T), RS1000226919 (2:169819307 CTT>C), RS1000350487 (2:169824868 C>T), RS1000399055 (2:169812515 C>T), RS1000532045 (2:169817460 T>C,G), RS1000693855 (2:169823833 T>C), RS1000795540 (2:169821823 T>A), RS1001127240 (2:169824026 A>G), RS1001168861 (2:169818222 A>G), RS1001306882 (2:169811411 G>A,T), RS1001383600 (2:169826175 G>GT), RS1001620275 (2:169818623 T>A), RS1001634843 (2:169820938 C>T), RS1001982902 (2:169823140 C>A)

Disease associations

OMIM: gene MIM:618628 | disease phenotypes: MIM:618665

GenCC curated gene-disease

DiseaseClassificationInheritance
intellectual developmental disorder, autosomal recessive 72StrongAutosomal recessive
autosomal recessive primary microcephalySupportiveAutosomal recessive

Mondo (2): intellectual developmental disorder, autosomal recessive 72 (MONDO:0032860), autosomal recessive primary microcephaly (MONDO:0016660)

Orphanet (0):

HPO phenotypes

17 total (17 of 17 shown, HPO-id order):

HPOTerm
HP:0000076Vesicoureteral reflux
HP:0000122Unilateral renal agenesis
HP:0000219Thin upper lip vermilion
HP:0000252Microcephaly
HP:0000340Sloping forehead
HP:0000582Upslanted palpebral fissure
HP:0001263Global developmental delay
HP:0001274Agenesis of corpus callosum
HP:0001302Pachygyria
HP:0001347Hyperreflexia
HP:0001510Growth delay
HP:0002119Ventriculomegaly
HP:0002282Gray matter heterotopia
HP:0003103Abnormal cortical bone morphology
HP:0004322Short stature
HP:0007333Hypoplasia of the frontal lobes
HP:0010864Severe intellectual disability

GWAS associations

1 associations (top):

StudyTraitp-value
GCST009190_3Medial orbital frontal cortex volume7.000000e-06

MeSH disease descriptors (1)

DescriptorNameTree numbers
C579935Autosomal Recessive Primary Microcephaly (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5483089 (PROTEIN COMPLEX)

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression, affects cotreatment, increases abundance2
Air Pollutantsaffects expression, increases abundance, decreases expression2
Leadaffects splicing, increases expression2
Tretinoindecreases expression2
Valproic Acidaffects expression, increases methylation2
aristolochic acid Idecreases expression1
bisphenol Aaffects expression1
cobaltous chloridedecreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
beta-methylcholineaffects expression1
chloropicrinincreases expression1
jinfukangdecreases expression1
Acetaminophendecreases expression1
Ethanolincreases abundance, affects cotreatment, decreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazineincreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Manganeseaffects cotreatment, increases abundance, increases expression1
Methyl Methanesulfonatedecreases expression1
Ozoneincreases abundance, affects expression1
Polycyclic Aromatic Hydrocarbonsaffects cotreatment, decreases expression, increases abundance1
Potassium Dichromatedecreases expression1
Quercetindecreases expression1
Smokedecreases expression, increases abundance1
Thiramdecreases expression1
Cyclosporineincreases expression1
Sodium Seleniteincreases expression1
Particulate Matteraffects cotreatment, decreases expression, increases abundance1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5317819BindingInhibition of human METTL5/TRM112 using 5’-UCG UAA CAA GGU UU-3’ as substrate and SAM as cosubstrate at 10 uM incubated for 1 hrSystematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile-Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence. — J Med Chem

Cellosaurus cell lines

8 cell lines: 5 cancer cell line, 3 embryonic stem cell

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

CellosaurusNameCategorySex
CVCL_A4D1SEES3-1V human METTL5, clone1Embryonic stem cellMale
CVCL_A4D2SEES3-1V human METTL5, clone2Embryonic stem cellMale
CVCL_A4D3SEES3-1V human METTL5, clone3Embryonic stem cellMale
CVCL_B1X1Abcam HeLa METTL5 KOCancer cell lineFemale
CVCL_SY05HAP1 METTL5 (-) 1Cancer cell lineMale
CVCL_SY06HAP1 METTL5 (-) 2Cancer cell lineMale
CVCL_SY07HAP1 METTL5 (-) 3Cancer cell lineMale
CVCL_SY08HAP1 METTL5 (-) 5Cancer cell lineMale

Clinical trials (associated diseases)

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