Seroatlas · Human Serome Atlas

LCMT2

tRNA wybutosine-synthesizing protein 4

Also known as: KIAA0547, MGC9534, PPM2, TYW4, TYW4_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: O60294
Gene: LCMT2
Ensembl: ENSG00000168806
Chromosome: 15
Canonical length: 686 aa
Protein class: Enzymes, Plasma proteins, Predicted intracellular proteins
Subcellular location: Cytosol

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

686 residues, UniProt reviewed canonical sequence.

>O60294|LCMT2
     1  MGPRSRERRA GAVQNTNDSS ALSKRSLAAR GYVQDPFAAL LVPGAARRAP LIHRGYYVRA
    61  RAVRHCVRAF LEQIGAPQAA LRAQILSLGA GFDSLYFRLK TAGRLARAAV WEVDFPDVAR
   121  RKAERIGETP ELCALTGPFE RGEPASALCF ESADYCILGL DLRQLQRVEE ALGAAGLDAA
   181  SPTLLLAEAV LTYLEPESAA ALIAWAAQRF PNALFVVYEQ MRPQDAFGQF MLQHFRQLNS
   241  PLHGLERFPD VEAQRRRFLQ AGWTACGAVD MNEFYHCFLP AEERRRVENI EPFDEFEEWH
   301  LKCAHYFILA ASRGDTLSHT LVFPSSEAFP RVNPASPSGV FPASVVSSEG QVPNLKRYGH
   361  ASVFLSPDVI LSAGGFGEQE GRHCRVSQFH LLSRDCDSEW KGSQIGSCGT GVQWDGRLYH
   421  TMTRLSESRV LVLGGRLSPV SPALGVLQLH FFKSEDNNTE DLKVTITKAG RKDDSTLCCW
   481  RHSTTEVSCQ NQEYLFVYGG RSVVEPVLSD WHFLHVGTMA WVRIPVEGEV PEARHSHSAC
   541  TWQGGALIAG GLGASEEPLN SVLFLRPISC GFLWESVDIQ PPITPRYSHT AHVLNGKLLL
   601  VGGIWIHSSS FPGVTVINLT TGLSSEYQID TTYVPWPLML HNHTSILLPE EQQLLLLGGG
   661  GNCFSFGTYF NPHTVTLDLS SLSAGQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LCMT2 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.22
Highest tissue expression: 8.6 nTPM

Expression across tissuesHPA

Tissue

tonsil: 8.6 nTPM
parathyroid gland: 7.5 nTPM
thymus: 7.2 nTPM
epididymis: 7.1 nTPM
kidney: 6.9 nTPM
retina: 6.8 nTPM

Single-cell type

early primary spermatocytes: 26 nCPM
esophageal apical cells: 15 nCPM
erythrocyte progenitors: 11 nCPM
retinal pigment epithelial cells: 8.5 nCPM
cardiomyocytes: 8 nCPM
differentiating spermatogonia: 8 nCPM

Immune cell

naive CD4 T-cell: 6 nTPM
myeloid DC: 4.4 nTPM
naive CD8 T-cell: 4.1 nTPM
memory CD4 T-cell: 3.9 nTPM
eosinophil: 3.8 nTPM
naive B-cell: 3.5 nTPM

Brain region

cerebellum: 9.4 nTPM
choroid plexus: 8.5 nTPM
hypothalamus: 8.2 nTPM
pons: 6.7 nTPM
midbrain: 6.3 nTPM
medulla oblongata: 6.2 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 1.47
gnomAD pLI: 0
gnomAD missense Z: -1.97
DepMap mean gene effect: -0.19
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

tRNA methyltransferase activity

Cellular components

cytoplasm

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of LCMT2 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

RNF144B

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads LCMT2 as an antibody target. Whether an autoantibody or antibody against LCMT2 could matter depends on whether native LCMT2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LCMT2 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label LCMT2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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