LCMT2

leucine carboxyl methyltransferase 2, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 15:43323649-43330582

Links

ENSG00000168806 ∙ NCBI:9836 ∙ OMIM:611246 ∙ HGNC:17558 ∙ Uniprot:O60294 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LCMT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCMT2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			60	4		64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	4	0

Variants in LCMT2

This is a list of pathogenic ClinVar variants found in the LCMT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-43328482-A-G		not specified	Uncertain significance (Apr 17, 2024)
15-43328509-C-G		not specified	Uncertain significance (Jan 11, 2023)
15-43328619-C-T		not specified	Uncertain significance (Dec 01, 2022)
15-43328670-T-C		not specified	Uncertain significance (Dec 01, 2022)
15-43328788-T-C		not specified	Uncertain significance (Mar 25, 2024)
15-43328791-G-A		not specified	Uncertain significance (May 24, 2023)
15-43328833-C-T		not specified	Uncertain significance (Aug 12, 2021)
15-43328848-T-A		not specified	Uncertain significance (Oct 26, 2022)
15-43328859-C-T		not specified	Uncertain significance (Mar 31, 2024)
15-43328869-T-C		not specified	Uncertain significance (Mar 01, 2023)
15-43328899-G-A		not specified	Uncertain significance (Jun 18, 2021)
15-43328931-G-A		not specified	Uncertain significance (Feb 17, 2024)
15-43328940-C-T		not specified	Likely benign (Dec 11, 2023)
15-43328947-G-A		not specified	Uncertain significance (Jan 31, 2024)
15-43328983-C-T		not specified	Uncertain significance (Feb 22, 2023)
15-43329046-G-T		not specified	Uncertain significance (Nov 22, 2023)
15-43329063-G-C		not specified	Uncertain significance (Jul 31, 2023)
15-43329106-G-C		not specified	Uncertain significance (Jun 07, 2024)
15-43329111-T-G		not specified	Uncertain significance (May 29, 2024)
15-43329145-G-A		not specified	Uncertain significance (Mar 28, 2024)
15-43329202-C-T		not specified	Uncertain significance (Apr 28, 2022)
15-43329316-G-A		not specified	Uncertain significance (Dec 26, 2023)
15-43329326-C-G		not specified	Uncertain significance (Mar 12, 2024)
15-43329396-A-G		not specified	Uncertain significance (May 15, 2023)
15-43329403-C-T		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCMT2	protein_coding	protein_coding	ENST00000305641	1	2830

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.63e-15	0.00925	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.97	499	390	1.28	0.0000193	4396
Missense in Polyphen		150	117.95	1.2717		1367
Synonymous	-1.40	189	166	1.14	0.00000815	1497
Loss of Function	-0.138	22	21.3	1.03	0.00000113	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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 eukaryotic phenylalanine tRNA (By similarity). May methylate the carboxyl group of leucine residues to form alpha- leucine ester residues. {ECO:0000250}.
• Pathway: Synthesis of wybutosine at G37 of tRNA(Phe);tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA;wybutosine biosynthesis (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.925
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.5

Haploinsufficiency Scores

• pHI: 0.0779
• hipred: N
• hipred_score: 0.170
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.719

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lcmt2

Gene ontology

• Biological process: tRNA modification;C-terminal protein methylation;tRNA methylation;wybutosine biosynthetic process
• Cellular component: cytoplasm
• Molecular function: protein binding;tRNA methyltransferase activity;protein C-terminal leucine carboxyl O-methyltransferase activity