LCMT1

leucine carboxyl methyltransferase 1, the group of Protein phosphatase 2 modulatory subunits|7BS protein methyltransferases

Basic information

Region (hg38): 16:25111731-25178231

Links

ENSG00000205629 ∙ NCBI:51451 ∙ OMIM:610286 ∙ HGNC:17557 ∙ Uniprot:Q9UIC8 ∙ 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 LCMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCMT1 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	13	1	1

Variants in LCMT1

This is a list of pathogenic ClinVar variants found in the LCMT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-25111909-C-A		not specified	Uncertain significance (Aug 19, 2024)
16-25111915-C-T		not specified	Uncertain significance (Oct 12, 2021)
16-25111918-C-T		not specified	Uncertain significance (Mar 05, 2024)
16-25111950-G-T		not specified	Uncertain significance (Aug 02, 2022)
16-25128480-C-T		not specified	Uncertain significance (Sep 10, 2024)
16-25128509-T-C		not specified	Uncertain significance (Dec 14, 2023)
16-25132411-C-T		not specified	Uncertain significance (Sep 22, 2023)
16-25132414-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-25132453-G-A		not specified	Uncertain significance (Jul 30, 2024)
16-25140204-G-A		not specified	Uncertain significance (Jul 14, 2024)
16-25140213-C-A		not specified	Uncertain significance (Dec 16, 2021)
16-25140216-A-G		not specified	Uncertain significance (Apr 08, 2024)
16-25140226-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-25140239-C-G		not specified	Uncertain significance (May 30, 2024)
16-25161138-T-C		not specified	Uncertain significance (Mar 20, 2024)
16-25161210-AT-A			Benign (Jun 15, 2018)
16-25164713-G-A		not specified	Uncertain significance (Mar 19, 2024)
16-25169128-G-T		not specified	Uncertain significance (Jul 20, 2021)
16-25169163-C-A		not specified	Uncertain significance (Mar 13, 2023)
16-25169163-C-T		not specified	Uncertain significance (Feb 17, 2023)
16-25170756-G-T		not specified	Uncertain significance (Feb 28, 2023)
16-25170759-G-A		not specified	Uncertain significance (Sep 18, 2024)
16-25170790-G-A		not specified	Uncertain significance (May 05, 2023)
16-25174990-G-A		not specified	Likely benign (Aug 02, 2021)
16-25175023-G-A		not specified	Uncertain significance (May 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCMT1	protein_coding	protein_coding	ENST00000399069	11	66503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000179	0.973	124625	0	28	124653	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.628	160	184	0.870	0.00000965	2181
Missense in Polyphen		36	56.115	0.64154		700
Synonymous	-0.0607	70	69.4	1.01	0.00000375	617
Loss of Function	2.01	11	20.9	0.526	0.00000110	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000470	0.000397
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000167
Finnish	0.000105	0.0000928
European (Non-Finnish)	0.0000621	0.0000619
Middle Eastern	0.000168	0.000167
South Asian	0.000232	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Methylates the carboxyl group of the C-terminal leucine residue of protein phosphatase 2A catalytic subunits to form alpha-leucine ester residues. {ECO:0000269|PubMed:10600115}.
• Pathway: Cyclin A/B1/B2 associated events during G2/M transition;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.785
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.0224
• hipred: Y
• hipred_score: 0.669
• ghis: 0.568

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lcmt1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); renal/urinary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;cellular protein modification process;protein methylation;C-terminal protein methylation;regulation of glucose metabolic process;negative regulation of protein complex assembly;regulation of apoptotic process;regulation of mitotic cell cycle spindle assembly checkpoint
• Cellular component: nucleoplasm;cytosol
• Molecular function: protein C-terminal carboxyl O-methyltransferase activity;protein binding;S-adenosylmethionine-dependent methyltransferase activity;protein C-terminal leucine carboxyl O-methyltransferase activity