LCMT2

Chr 15

leucine carboxyl methyltransferase 2

Also known as: PPM2, TYW4

NCBI Gene: 9836 ENSG00000168806 UniProt: O60294 OMIM: 611246

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 hypermodified guanosine Wybutosine (yW). [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

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P/LP submissions

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P/LP missense

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LOEUF

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Mechanism

Some data sources returned errors (1)

gnomad: Error: gnomAD API error: 400

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in LCMT2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 54

1,176 rare PASS variants

Rare truncating (LoF)

1 in 480

170 rare PASS variants

Rare synonymous (reference)

1 in 170

455 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for LCMT2. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 75	1 in 490
South Asian	~43k	1 in 53	1 in 350
Remaining (unassigned)	~30k	1 in 49	1 in 400
European (Finnish)	~27k	1 in 190	1 in 1,900
Admixed American	~22k	1 in 55	1 in 320
African / African American	~21k	1 in 33	1 in 520
East Asian	~20k	1 in 66	1 in 1,200
Ashkenazi Jewish	~13k	1 in 390	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 55	1 in 580

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.