LCMT2 (leucine carboxyl methyltransferase 2)

Gene

• Entrez ID: 9836
• Gene name: Leucine carboxyl methyltransferase 2
• Gene symbol: LCMT2
• Synonyms (NCBI Gene): PPM2, TYW4
• Chromosome: 15
• Chromosome location: 15q15.3
• Summary: The protein encoded by this intronless gene belongs to the highly variable methyltransferase superfamily. This gene is the inferred homolog of the Saccharomyces cerevisiae carboxymethyltransferase gene PPM2 that is essential for the synthesis of the hyper

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1105748	hsa-miR-2110	CLIP-seq
MIRT1105749	hsa-miR-2392	CLIP-seq
MIRT1105750	hsa-miR-3153	CLIP-seq
MIRT1105751	hsa-miR-3173-3p	CLIP-seq
MIRT1105752	hsa-miR-4271	CLIP-seq
MIRT1105753	hsa-miR-4725-3p	CLIP-seq
MIRT1105754	hsa-miR-765	CLIP-seq
MIRT1550692	hsa-miR-1207-3p	CLIP-seq
MIRT1550693	hsa-miR-4252	CLIP-seq
MIRT1550694	hsa-miR-4701-5p	CLIP-seq
MIRT1550695	hsa-miR-588	CLIP-seq
MIRT2029193	hsa-miR-1206	CLIP-seq
MIRT2029194	hsa-miR-134	CLIP-seq
MIRT2029195	hsa-miR-3117-5p	CLIP-seq
MIRT2029196	hsa-miR-3118	CLIP-seq
MIRT2029197	hsa-miR-3164	CLIP-seq
MIRT2029198	hsa-miR-340	CLIP-seq
MIRT2029199	hsa-miR-4307	CLIP-seq
MIRT1550694	hsa-miR-4701-5p	CLIP-seq
MIRT2029200	hsa-miR-548g	CLIP-seq
MIRT2029201	hsa-miR-579	CLIP-seq
MIRT1550695	hsa-miR-588	CLIP-seq
MIRT2029202	hsa-miR-892a	CLIP-seq
MIRT2029203	hsa-miR-943	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25910212
GO:0005737	Component	Cytoplasm	TAS
GO:0006400	Process	TRNA modification	TAS
GO:0008033	Process	TRNA processing	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008175	Function	TRNA methyltransferase activity	IBA
GO:0008175	Function	TRNA methyltransferase activity	TAS
GO:0016740	Function	Transferase activity	IEA
GO:0030488	Process	TRNA methylation	IBA
GO:0031591	Process	Wybutosine biosynthetic process	IBA
GO:0032259	Process	Methylation	IEA

Other IDs

• MIM: 611246
• HGNC: 17558
• e!Ensembl: ENSG00000168806

Protein

• UniProt ID: O60294
• Protein name: tRNA wybutosine-synthesizing protein 4 (tRNA yW-synthesizing protein 4) (EC 2.1.1.290) (EC 2.3.1.231) (Leucine carboxyl methyltransferase 2) (tRNA(Phe) (7-(3-amino-3-(methoxycarbonyl)propyl)wyosine(37)-N)-methoxycarbonyltransferase) (tRNA(Phe) (7-(3-amino
• Protein function: Probable S-adenosyl-L-methionine-dependent methyltransferase that acts as a component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eu
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04072	LCM	12 → 207	Leucine carboxyl methyltransferase	Family
  PF13964	Kelch_6	533 → 586		Repeat

• Sequence:

  MGPRSRERRAGAVQNTNDSSALSKRSLAARGYVQDPFAALLVPGAARRAPLIHRGYYVRA
  RAVRHCVRAFLEQIGAPQAALRAQILSLGAGFDSLYFRLKTAGRLARAAVWEVDFPDVAR
  RKAERIGETPELCALTGPFERGEPASALCFESADYCILGLDLRQLQRVEEALGAAGLDAA
  SPTLLLAEAVLTYLEPESAAALIAWAAQRFPNALFVVYEQMRPQDAFGQFMLQHFRQLNS
  PLHGLERFPDVEAQRRRFLQAGWTACGAVDMNEFYHCFLPAEERRRVENIEPFDEFEEWH
  LKCAHYFILAASRGDTLSHTLVFPSSEAFPRVNPASPSGVFPASVVSSEGQVPNLKRYGH
  ASVFLSPDVILSAGGFGEQEGRHCRVSQFHLLSRDCDSEWKGSQIGSCGTGVQWDGRLYH
  TMTRLSESRVLVLGGRLSPVSPALGVLQLHFFKSEDNNTEDLKVTITKAGRKDDSTLCCW
  RHSTTEVSCQNQEYLFVYGGRSVVEPVLSDWHFLHVGTMAWVRIPVEGEVPEARHSHSAC
  TWQGGALIAGGLGASEEPLNSVLFLRPISCGFLWESVDIQPPITPRYSHTAHVLNGKLLL
  VGGIWIHSSSFPGVTVINLTTGLSSEYQIDTTYVPWPLMLHNHTSILLPEEQQLLLLGGG
  GNCFSFGTYFNPHTVTLDLSSLSAGQ

• Sequence length: 686

Pathways

Reactome:

Synthesis of wybutosine at G37 of tRNA(Phe)

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anodontia	Anodontia	Pubtator	28803425	Associate	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	28803425	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	28803425	Associate	★☆☆☆☆ Found in Text Mining only