mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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	Gene Summary
	Ligand Binding Site Mutation Information
	Protein Structure Related Information
	Gene Expression and Gene-Gene Network
	Phenotype Information
	Pharmacological Information
	Conservation Information for LBS

Gene summary for TRMT10A

Gene summary

Basic gene Info.	Gene symbol	TRMT10A
	Gene name	tRNA methyltransferase 10 homolog A (S. cerevisiae)
	Synonyms	HEL-S-88\|MSSGM\|RG9MTD2\|TRM10
	Cytomap	UCSC genome browser: 4q23
	Type of gene	protein-coding
	RefGenes	NM_001134665.2, NM_001134666.2,NM_152292.4,
	Description	RNA (guanine-9-)-methyltransferase domain-containing protein 2epididymis secretory protein Li 88tRNA methyltransferase 10 homolog A
	Modification date	20141207
dbXrefs	MIM : 616013
	HGNC : HGNC
	Ensembl : ENSG00000145331
	HPRD : 15241
	Vega : OTTHUMG00000131025
Protein	UniProt: Q8TBZ6 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TRMT10A
	BioGPS: 93587
Pathway	NCI Pathway Interaction Database: TRMT10A
	KEGG: TRMT10A
	REACTOME: TRMT10A
	Pathway Commons: TRMT10A
Context	iHOP: TRMT10A
	ligand binding site mutation search in PubMed: TRMT10A
	UCL Cancer Institute: TRMT10A
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID

GO Term

PubMed ID

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Ligand binding site mutations for TRMT10A

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
S188	D189G	HNSC	1
L186	L186F	SKCM	1
T187	T187M	UCEC	1
K244	R243Q	UCEC	1

cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.

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Protein structure related information for TRMT10A

Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
(ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)

: nsSNV at non-LBS

: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.

LBS	AAchange of nsSNV	Relative stability change
L186	L186F	-1.4117197
K244	R243Q	-1.0917698
S188	D189G	-0.93941628
T187	T187M	-0.48888246

(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for TRMT10A from PDB

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Differential gene expression and gene-gene network for TRMT10A

Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)

* Left PPI network was created from samples with mutations in the LBS of TRMT10A and the right PPI network was created from samples without mutations in the LBS of TRMT10A. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

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Phenotype information for TRMT10A

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for TRMT10A

Drug information targeting mutLBSgene (Approved drugs only)

Drug status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of TRMT10A go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
SAH		S-ADENOSYL-L-HOMOCYSTEINE	4fmw	A	L186 T187 S188 K244
SAH		S-ADENOSYL-L-HOMOCYSTEINE	4fmw	B	L186 T187 S188 K244

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Conservation information for LBS of TRMT10A

Multiple alignments for Q8TBZ6 in multiple species

LBS	AA sequence	# species	Species
D210	IGGLVDHNHHK	4	Homo sapiens, Xenopus tropicalis, Rattus norvegicus, Bos taurus
D210	VGGIVDKNRHK	2	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
D210	IGGLVDHNHFK	1	Drosophila melanogaster
D210	VGGIVDKNRYK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D210	IGAIVDKNRYK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D210	IGGLVDHSHHK	1	Mus musculus
G206	KAYVIGGLVDH	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
G206	TTYIVGGIVDK	2	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
G206	CTYVIGGLVDH	1	Drosophila melanogaster
G206	MRYIVGGIVDK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G206	KIYIIGAIVDK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G206	KAYIIGGLVDH	1	Xenopus tropicalis
H214	VDHNHHKGLTY	2	Homo sapiens, Bos taurus
H214	VDHNHFKGLCH	1	Drosophila melanogaster
H214	VDKNRYKELCL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H214	VDKNRHKNLCY	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
H214	VDKNRHKALCY	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H214	VDKNRYKNLCQ	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H214	VDHNHHKGITY	1	Xenopus tropicalis
H214	VDHSHHKGLTF	1	Mus musculus
H214	VDHNHHKGLTF	1	Rattus norvegicus
I205	SKAYVIGGLVD	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
I205	GTTYIVGGIVD	2	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
I205	GCTYVIGGLVD	1	Drosophila melanogaster
I205	GMRYIVGGIVD	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I205	DKIYIIGAIVD	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I205	TKAYIIGGLVD	1	Xenopus tropicalis
K244	KMNSRKVLAVN	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
K244	DMKTRAVLSTY	1	Drosophila melanogaster
K244	NLEGRRVLTTT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K244	NLAGRKVLTTS	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
K244	KLCGRKVLTTT	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
K244	KITDRKILTVN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K244	KMNTRKVLAVN	1	Xenopus tropicalis
L186	EDLVYLTSDSP	3	Xenopus tropicalis, Mus musculus, Rattus norvegicus
L186	EDLIYLTSDSP	2	Homo sapiens, Bos taurus
L186	SQLVYLTCESD	1	Drosophila melanogaster
L186	DKIVYLTADTE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L186	ENAVYLTADTE	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
L186	TNAVYLTADTD	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L186	EKLVYLSADSD	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L208	YVIGGLVDHNH	4	Homo sapiens, Drosophila melanogaster, Rattus norvegicus, Bos taurus
L208	YIVGGIVDKNR	3	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L208	YIIGAIVDKNR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L208	YIIGGLVDHNH	1	Xenopus tropicalis
L208	YVIGGLVDHSH	1	Mus musculus
L217	NHHKGLTYKQA	2	Homo sapiens, Bos taurus
L217	NHFKGLCHSRA	1	Drosophila melanogaster
L217	NRYKELCLKKA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L217	NRHKNLCYNKA	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
L217	NRHKALCYNKA	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L217	NRYKNLCQNKA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L217	NHHKGITYKKA	1	Xenopus tropicalis
L217	SHHKGLTFKQA	1	Mus musculus
L217	NHHKGLTFKQA	1	Rattus norvegicus
L232	INHAQLPLGNF	1	Homo sapiens
L232	LTTARLPLSEH	1	Drosophila melanogaster
L232	IPTRRLPIDEY	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L232	IPTKRLPIGEF	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
L232	IPTRRLPIGEY	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L232	IKTAKLPIDEY	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L232	ISHAQLPLGNF	1	Xenopus tropicalis
L232	IEHAQLPLADF	1	Mus musculus
L232	IKHAQLPLAEF	1	Rattus norvegicus
L232	IDHAQLPLGNF	1	Bos taurus
L234	HAQLPLGNFVK	3	Homo sapiens, Xenopus tropicalis, Bos taurus
L234	TARLPLSEHVD	1	Drosophila melanogaster
L234	TRRLPIDEYIN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L234	TKRLPIGEFIN	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
L234	TRRLPIGEYIK	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L234	TAKLPIDEYIK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L234	HAQLPLADFVK	1	Mus musculus
L234	HAQLPLAEFVK	1	Rattus norvegicus
L246	NSRKVLAVNHV	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
L246	KTRAVLSTYHV	1	Drosophila melanogaster
L246	EGRRVLTTTHV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L246	AGRKVLTTSHM	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
L246	CGRKVLTTTHV	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L246	TDRKILTVNQV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L246	NTRKVLAVNHV	1	Xenopus tropicalis
Q231	GINHAQLPLGN	1	Homo sapiens
Q231	GLTTARLPLSE	1	Drosophila melanogaster
Q231	GIPTRRLPIDE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q231	NIPTKRLPIGE	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Q231	GIPTRRLPIGE	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
Q231	GIKTAKLPIDE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q231	GISHAQLPLGN	1	Xenopus tropicalis
Q231	GIEHAQLPLAD	1	Mus musculus
Q231	GIKHAQLPLAE	1	Rattus norvegicus
Q231	GIDHAQLPLGN	1	Bos taurus
S188	LIYLTSDSPNI	2	Homo sapiens, Bos taurus
S188	LVYLTSDSPNV	2	Mus musculus, Rattus norvegicus
S188	LVYLTCESDRV	1	Drosophila melanogaster
S188	IVYLTADTEEK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S188	AVYLTADTEEK	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
S188	AVYLTADTDET	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
S188	LVYLSADSDNT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S188	LVYLTSDSPEV	1	Xenopus tropicalis
T187	DLIYLTSDSPN	2	Homo sapiens, Bos taurus
T187	DLVYLTSDSPN	2	Mus musculus, Rattus norvegicus
T187	QLVYLTCESDR	1	Drosophila melanogaster
T187	KIVYLTADTEE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T187	NAVYLTADTEE	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
T187	NAVYLTADTDE	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
T187	KLVYLSADSDN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T187	DLVYLTSDSPE	1	Xenopus tropicalis
T218	HHKGLTYKQAS	2	Homo sapiens, Bos taurus
T218	HFKGLCHSRAT	1	Drosophila melanogaster
T218	RYKELCLKKAQ	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T218	RHKNLCYNKAK	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
T218	RHKALCYNKAK	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
T218	RYKNLCQNKAS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T218	HHKGITYKKAL	1	Xenopus tropicalis
T218	HHKGLTFKQAT	1	Mus musculus
T218	HHKGLTFKQAS	1	Rattus norvegicus
V245	MNSRKVLAVNH	4	Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
V245	MKTRAVLSTYH	1	Drosophila melanogaster
V245	LEGRRVLTTTH	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V245	LAGRKVLTTSH	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
V245	LCGRKVLTTTH	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
V245	ITDRKILTVNQ	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V245	MNTRKVLAVNH	1	Xenopus tropicalis
V248	RKVLAVNHVFE	5	Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus, Bos taurus
V248	RAVLSTYHVFE	1	Drosophila melanogaster
V248	RRVLTTTHVVQ	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V248	RKVLTTSHMVQ	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
V248	RKVLTTTHVIQ	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
V248	RKILTVNQVFE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V251	LAVNHVFEIIL	5	Homo sapiens, Xenopus tropicalis, Mus musculus, Rattus norvegicus, Bos taurus
V251	LSTYHVFELLT	1	Drosophila melanogaster
V251	LTTTHVVQLML	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V251	LTTSHMVQLML	1	Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
V251	LTTTHVIQIML	1	Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
V251	LTVNQVFEILS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)