TRMT10A (tRNA methyltransferase 10A) - Rat Genome Database

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Gene: TRMT10A (tRNA methyltransferase 10A) Homo sapiens
Analyze
Symbol: TRMT10A
Name: tRNA methyltransferase 10A
RGD ID: 1319496
HGNC Page HGNC
Description: Enables tRNA (guanine(9)-N(1))-methyltransferase activity and tRNA binding activity. Involved in tRNA N1-guanine methylation. Located in actin cytoskeleton; cytosol; and nuclear lumen.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: epididymis secretory protein Li 88; FLJ20325; HEL-S-88; MGC27034; MSSGM; MSSGM1; RG9MTD2; RNA (guanine-9-) methyltransferase domain containing 2; RNA (guanine-9-)-methyltransferase domain-containing protein 2; TRM10; tRNA (guanine(9)-N(1))-methyltransferase TRMT10A; tRNA methyltransferase 10 homolog A
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38499,546,711 - 99,564,039 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl499,546,709 - 99,564,039 (-)EnsemblGRCh38hg38GRCh38
GRCh374100,467,868 - 100,485,196 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364100,686,904 - 100,703,848 (-)NCBINCBI36hg18NCBI36
Build 344100,825,061 - 100,842,003NCBI
Celera497,765,280 - 97,782,608 (-)NCBI
Cytogenetic Map4q23NCBI
HuRef496,205,953 - 96,223,232 (-)NCBIHuRef
CHM1_14100,444,338 - 100,461,662 (-)NCBICHM1_1
T2T-CHM13v2.04102,861,479 - 102,878,808 (-)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
actin cytoskeleton  (IDA)
cytosol  (IBA,IDA)
extracellular exosome  (HDA)
nucleolus  (IDA,IEA)
nucleoplasm  (IBA,IDA)
nucleus  (IBA,IDA,IEA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Abnormality of the nervous system  (IAGP)
Anteverted nares  (IAGP)
Autosomal recessive inheritance  (IAGP)
Axial hypotonia  (IAGP)
Blue sclerae  (IAGP)
Brisk reflexes  (IAGP)
Broad-based gait  (IAGP)
Cerebellar hypoplasia  (IAGP)
Clinodactyly  (IAGP)
Delayed myelination  (IAGP)
Delayed puberty  (IAGP)
Delayed thelarche  (IAGP)
Deviation of the 5th toe  (IAGP)
Diabetes mellitus  (IAGP)
Distal muscle weakness  (IAGP)
Dorsocervical fat pad  (IAGP)
Down-sloping shoulders  (IAGP)
Downslanted palpebral fissures  (IAGP)
Downturned corners of mouth  (IAGP)
Epicanthus  (IAGP)
Fine hair  (IAGP)
Full cheeks  (IAGP)
Global developmental delay  (IAGP)
High pitched voice  (IAGP)
Hyperinsulinemic hypoglycemia  (IAGP)
Hypoglycemia  (IAGP)
Hypoplasia of teeth  (IAGP)
Hypoplasia of the brainstem  (IAGP)
Hypoplasia of the corpus callosum  (IAGP)
Hypotelorism  (IAGP)
Hypothyroidism  (IAGP)
Intellectual disability  (IAGP)
Intellectual disability, severe  (IAGP)
Intrauterine growth retardation  (IAGP)
Joint laxity  (IAGP)
Ketosis  (IAGP)
Kyphoscoliosis  (IAGP)
Long philtrum  (IAGP)
Low anterior hairline  (IAGP)
Macrotia  (IAGP)
Microcephaly  (IAGP)
Micrognathia  (IAGP)
Motor delay  (IAGP)
Narrow face  (IAGP)
Narrow forehead  (IAGP)
Narrow mouth  (IAGP)
Oligodontia  (IAGP)
Osteoporosis  (IAGP)
Pectus excavatum  (IAGP)
Pes valgus  (IAGP)
Poor speech  (IAGP)
Primary amenorrhea  (IAGP)
Primary microcephaly  (IAGP)
Proportionate short stature  (IAGP)
Round face  (IAGP)
Scoliosis  (IAGP)
Seizure  (IAGP)
Sensorineural hearing impairment  (IAGP)
Severe demyelination of the white matter  (IAGP)
Severe postnatal growth retardation  (IAGP)
Short neck  (IAGP)
Short nose  (IAGP)
Short philtrum  (IAGP)
Short stature  (IAGP)
Slender finger  (IAGP)
Slender toe  (IAGP)
Small for gestational age  (IAGP)
Sparse hair  (IAGP)
Spastic paraparesis  (IAGP)
Synophrys  (IAGP)
Thin upper lip vermilion  (IAGP)
Wide nose  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. RGD HPO Phenotype Annotation Pipeline RGD automated import pipeline for human HPO-to-gene-to-disease annotations
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:19056867   PMID:20459617   PMID:21873635   PMID:22658674   PMID:22863883   PMID:23042678   PMID:24204302   PMID:25053765   PMID:26297882   PMID:26496610   PMID:26526202   PMID:29507755  
PMID:30247717   PMID:31292261   PMID:32213595   PMID:32296183   PMID:32392304   PMID:33961781  


Genomics

Comparative Map Data
TRMT10A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38499,546,711 - 99,564,039 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl499,546,709 - 99,564,039 (-)EnsemblGRCh38hg38GRCh38
GRCh374100,467,868 - 100,485,196 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364100,686,904 - 100,703,848 (-)NCBINCBI36hg18NCBI36
Build 344100,825,061 - 100,842,003NCBI
Celera497,765,280 - 97,782,608 (-)NCBI
Cytogenetic Map4q23NCBI
HuRef496,205,953 - 96,223,232 (-)NCBIHuRef
CHM1_14100,444,338 - 100,461,662 (-)NCBICHM1_1
T2T-CHM13v2.04102,861,479 - 102,878,808 (-)NCBI
Trmt10a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393137,849,209 - 137,865,582 (+)NCBIGRCm39mm39
GRCm39 Ensembl3137,849,209 - 137,865,582 (+)Ensembl
GRCm383138,143,448 - 138,159,821 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3138,143,448 - 138,159,821 (+)EnsemblGRCm38mm10GRCm38
MGSCv373137,806,502 - 137,822,785 (+)NCBIGRCm37mm9NCBIm37
MGSCv363138,080,925 - 138,097,208 (+)NCBImm8
Celera3144,554,497 - 144,570,828 (+)NCBICelera
Cytogenetic Map3G3NCBI
Trmt10a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22226,669,445 - 226,684,166 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2226,669,832 - 226,684,151 (+)Ensembl
Rnor_6.02243,422,811 - 243,437,533 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2243,422,811 - 243,438,050 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02261,963,896 - 261,978,618 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42235,670,051 - 235,683,261 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2218,825,623 - 218,838,832 (+)NCBICelera
Cytogenetic Map2q44NCBI
Trmt10a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554968,026,569 - 8,037,802 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554968,021,747 - 8,037,562 (+)NCBIChiLan1.0ChiLan1.0
TRMT10A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14102,631,501 - 102,648,770 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4102,631,501 - 102,648,454 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0491,970,440 - 91,987,722 (-)NCBIMhudiblu_PPA_v0panPan3
TRMT10A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13221,554,096 - 21,570,894 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3221,555,045 - 21,570,338 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3220,325,736 - 20,343,112 (+)NCBI
ROS_Cfam_1.03221,774,481 - 21,792,045 (-)NCBI
ROS_Cfam_1.0 Ensembl3221,773,270 - 21,791,576 (-)Ensembl
UMICH_Zoey_3.13221,751,224 - 21,768,766 (-)NCBI
UNSW_CanFamBas_1.03221,538,921 - 21,556,250 (-)NCBI
UU_Cfam_GSD_1.03218,312,807 - 18,330,371 (+)NCBI
Trmt10a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530120,056,582 - 20,070,786 (+)NCBI
SpeTri2.0NW_0049365203,400,029 - 3,413,867 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRMT10A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8120,879,523 - 120,917,433 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18120,879,067 - 120,917,442 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28130,095,032 - 130,133,417 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TRMT10A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1747,689,865 - 47,706,540 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl747,691,555 - 47,701,748 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603726,154,118 - 26,171,617 (-)NCBIVero_WHO_p1.0
Trmt10a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248307,519,851 - 7,530,772 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046248307,515,810 - 7,529,980 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH102787  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh374100,467,997 - 100,468,116UniSTSGRCh37
Build 364100,687,020 - 100,687,139RGDNCBI36
Celera497,765,413 - 97,765,532RGD
Cytogenetic Map4q23UniSTS
HuRef496,206,086 - 96,206,205UniSTS
GeneMap99-GB4 RH Map4494.02UniSTS
STS-AA001648  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh374100,468,096 - 100,468,277UniSTSGRCh37
Build 364100,687,119 - 100,687,300RGDNCBI36
Celera497,765,512 - 97,765,693RGD
Cytogenetic Map4q23UniSTS
HuRef496,206,185 - 96,206,366UniSTS
GeneMap99-GB4 RH Map4490.71UniSTS
NCBI RH Map41161.2UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1887
Count of miRNA genes:600
Interacting mature miRNAs:668
Transcripts:ENST00000273962, ENST00000394876, ENST00000394877, ENST00000455368, ENST00000507394, ENST00000514547, ENST00000515831
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 27 7 5 241 6 4 3 17 21 165 49 1 1
Low 2410 2498 1716 619 1311 459 4345 2111 3676 395 1295 1563 174 1 1203 2781 4 2
Below cutoff 2 493 3 399 7 83 40 3 1 1 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_041774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001134665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001134666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001375880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001375881 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001375882 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_152292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047416418 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC083902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF106046 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK000332 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK313548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AW242551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC028373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068274 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB455183 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU668342 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000273962   ⟹   ENSP00000273962
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl499,546,727 - 99,563,668 (-)Ensembl
RefSeq Acc Id: ENST00000394876   ⟹   ENSP00000378342
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl499,546,711 - 99,564,039 (-)Ensembl
RefSeq Acc Id: ENST00000394877   ⟹   ENSP00000378343
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl499,546,709 - 99,564,017 (-)Ensembl
RefSeq Acc Id: ENST00000455368   ⟹   ENSP00000397551
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl499,553,813 - 99,563,730 (-)Ensembl
RefSeq Acc Id: ENST00000507394
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl499,557,689 - 99,563,672 (-)Ensembl
RefSeq Acc Id: ENST00000514547   ⟹   ENSP00000423628
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl499,553,831 - 99,563,723 (-)Ensembl
RefSeq Acc Id: ENST00000515831
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl499,556,146 - 99,557,530 (-)Ensembl
RefSeq Acc Id: NM_001134665   ⟹   NP_001128137
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38499,546,711 - 99,564,039 (-)NCBI
GRCh374100,467,864 - 100,485,189 (-)RGD
Celera497,765,280 - 97,782,608 (-)RGD
HuRef496,205,953 - 96,223,232 (-)RGD
CHM1_14100,444,338 - 100,461,687 (-)NCBI
T2T-CHM13v2.04102,861,479 - 102,878,808 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001134666   ⟹   NP_001128138
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38499,546,711 - 99,564,039 (-)NCBI
GRCh374100,467,864 - 100,485,189 (-)RGD
Celera497,765,280 - 97,782,608 (-)RGD
HuRef496,205,953 - 96,223,232 (-)RGD
CHM1_14100,444,338 - 100,461,687 (-)NCBI
T2T-CHM13v2.04102,861,479 - 102,878,808 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001375880   ⟹   NP_001362809
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38499,546,711 - 99,563,723 (-)NCBI
T2T-CHM13v2.04102,861,479 - 102,878,492 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001375881   ⟹   NP_001362810
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38499,546,711 - 99,563,723 (-)NCBI
T2T-CHM13v2.04102,861,479 - 102,878,492 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001375882   ⟹   NP_001362811
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38499,546,711 - 99,564,039 (-)NCBI
T2T-CHM13v2.04102,861,479 - 102,878,808 (-)NCBI
Sequence:
RefSeq Acc Id: NM_152292   ⟹   NP_689505
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38499,546,711 - 99,563,723 (-)NCBI
GRCh374100,467,864 - 100,485,189 (-)RGD
Build 364100,686,904 - 100,703,848 (-)NCBI Archive
Celera497,765,280 - 97,782,608 (-)RGD
HuRef496,205,953 - 96,223,232 (-)RGD
CHM1_14100,444,338 - 100,461,298 (-)NCBI
T2T-CHM13v2.04102,861,479 - 102,878,492 (-)NCBI
Sequence:
RefSeq Acc Id: XM_047416418   ⟹   XP_047272374
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38499,546,711 - 99,563,723 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001128137   ⟸   NM_001134665
- Peptide Label: isoform 1
- UniProtKB: Q8TBZ6 (UniProtKB/Swiss-Prot),   V9HVY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001128138   ⟸   NM_001134666
- Peptide Label: isoform 1
- UniProtKB: Q8TBZ6 (UniProtKB/Swiss-Prot),   V9HVY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_689505   ⟸   NM_152292
- Peptide Label: isoform 1
- UniProtKB: Q8TBZ6 (UniProtKB/Swiss-Prot),   V9HVY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001362811   ⟸   NM_001375882
- Peptide Label: isoform 2
RefSeq Acc Id: NP_001362810   ⟸   NM_001375881
- Peptide Label: isoform 1
RefSeq Acc Id: NP_001362809   ⟸   NM_001375880
- Peptide Label: isoform 1
RefSeq Acc Id: ENSP00000397551   ⟸   ENST00000455368
RefSeq Acc Id: ENSP00000273962   ⟸   ENST00000273962
RefSeq Acc Id: ENSP00000378343   ⟸   ENST00000394877
RefSeq Acc Id: ENSP00000378342   ⟸   ENST00000394876
RefSeq Acc Id: ENSP00000423628   ⟸   ENST00000514547
RefSeq Acc Id: XP_047272374   ⟸   XM_047416418
- Peptide Label: isoform X1
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8TBZ6-F1-model_v2 AlphaFold Q8TBZ6 1-339 view protein structure

Promoters
RGD ID:6868104
Promoter ID:EPDNEW_H7217
Type:initiation region
Name:TRMT10A_1
Description:tRNA methyltransferase 10A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H7218  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38499,563,723 - 99,563,783EPDNEW
RGD ID:6868106
Promoter ID:EPDNEW_H7218
Type:initiation region
Name:TRMT10A_2
Description:tRNA methyltransferase 10A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H7217  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38499,564,019 - 99,564,079EPDNEW
RGD ID:6802500
Promoter ID:HG_KWN:48796
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000394876,   ENST00000394877,   NM_000253,   NM_001134665,   NM_152292
Position:
Human AssemblyChrPosition (strand)Source
Build 364100,703,746 - 100,704,477 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q23(chr4:97972342-100038125)x3 copy number gain See cases [RCV000051632] Chr4:97972342..100038125 [GRCh38]
Chr4:98893493..100959282 [GRCh37]
Chr4:99112516..101178305 [NCBI36]
Chr4:4q23
uncertain significance
GRCh38/hg38 4q22.2-32.3(chr4:92913386-165299707)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|See cases [RCV000051775] Chr4:92913386..165299707 [GRCh38]
Chr4:93834537..166220859 [GRCh37]
Chr4:94053560..166440309 [NCBI36]
Chr4:4q22.2-32.3
pathogenic
GRCh38/hg38 4q22.3-28.3(chr4:96092893-136410207)x3 copy number gain See cases [RCV000051776] Chr4:96092893..136410207 [GRCh38]
Chr4:97014044..137331362 [GRCh37]
Chr4:97233067..137550812 [NCBI36]
Chr4:4q22.3-28.3
pathogenic
NM_001134665.3(TRMT10A):c.379C>T (p.Arg127Ter) single nucleotide variant Microcephaly, short stature, and impaired glucose metabolism 1 [RCV000144247] Chr4:99557386 [GRCh38]
Chr4:100478543 [GRCh37]
Chr4:4q23
pathogenic|likely pathogenic
NM_001134665.3(TRMT10A):c.616G>A (p.Gly206Arg) single nucleotide variant Inborn genetic diseases [RCV000624590]|Microcephaly, short stature, and impaired glucose metabolism 1 [RCV000144248] Chr4:99553814 [GRCh38]
Chr4:100474971 [GRCh37]
Chr4:4q23
pathogenic
GRCh38/hg38 4q21.21-24(chr4:80427023-100855441)x1 copy number loss See cases [RCV000137269] Chr4:80427023..100855441 [GRCh38]
Chr4:81348177..101776598 [GRCh37]
Chr4:81567201..101995621 [NCBI36]
Chr4:4q21.21-24
pathogenic
GRCh38/hg38 4q22.1-24(chr4:92610413-101521991)x1 copy number loss See cases [RCV000140412] Chr4:92610413..101521991 [GRCh38]
Chr4:93531564..102443148 [GRCh37]
Chr4:93750587..102662171 [NCBI36]
Chr4:4q22.1-24
pathogenic
NM_001134665.3(TRMT10A):c.679A>C (p.Ile227Leu) single nucleotide variant not provided [RCV001760765] Chr4:99550957 [GRCh38]
Chr4:100472114 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.79G>T (p.Glu27Ter) single nucleotide variant not provided [RCV000728879] Chr4:99559260 [GRCh38]
Chr4:100480417 [GRCh37]
Chr4:4q23
pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:12440-190904441)x3 copy number gain See cases [RCV000446653] Chr4:12440..190904441 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4q21.23-24(chr4:85805268-103678797)x1 copy number loss See cases [RCV000445741] Chr4:85805268..103678797 [GRCh37]
Chr4:4q21.23-24
pathogenic
NM_001134665.3(TRMT10A):c.206G>A (p.Arg69His) single nucleotide variant not provided [RCV000889564]|not specified [RCV000503318] Chr4:99558191 [GRCh38]
Chr4:100479348 [GRCh37]
Chr4:4q23
benign
NM_001134665.3(TRMT10A):c.955C>A (p.Pro319Thr) single nucleotide variant not provided [RCV000911862]|not specified [RCV000501506] Chr4:99549153 [GRCh38]
Chr4:100470310 [GRCh37]
Chr4:4q23
likely benign|uncertain significance
NM_001134665.3(TRMT10A):c.398G>A (p.Arg133Gln) single nucleotide variant Microcephaly, short stature, and impaired glucose metabolism 1 [RCV000764520]|not provided [RCV001410599]|not specified [RCV000501846] Chr4:99557367 [GRCh38]
Chr4:100478524 [GRCh37]
Chr4:4q23
likely benign|uncertain significance
NM_001134665.3(TRMT10A):c.866_868del (p.Ser289_His290delinsTyr) deletion not specified [RCV000503599] Chr4:99549240..99549242 [GRCh38]
Chr4:100470397..100470399 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.837T>A (p.Val279=) single nucleotide variant not specified [RCV000500403] Chr4:99549271 [GRCh38]
Chr4:100470428 [GRCh37]
Chr4:4q23
likely benign
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473) copy number gain See cases [RCV000510453] Chr4:68346..190957473 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4q22.1-24(chr4:92201567-103043808)x1 copy number loss See cases [RCV000511194] Chr4:92201567..103043808 [GRCh37]
Chr4:4q22.1-24
pathogenic
GRCh37/hg19 4q22.1-35.2(chr4:93071152-190957473)x3 copy number gain See cases [RCV000510970] Chr4:93071152..190957473 [GRCh37]
Chr4:4q22.1-35.2
pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:68346-190957473)x3 copy number gain See cases [RCV000512241] Chr4:68346..190957473 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190915650)x3 copy number gain not provided [RCV000743155] Chr4:49450..190915650 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:49450-190963766)x3 copy number gain not provided [RCV000743156] Chr4:49450..190963766 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
GRCh37/hg19 4p16.3-q35.2(chr4:11525-191028879)x3 copy number gain not provided [RCV000743147] Chr4:11525..191028879 [GRCh37]
Chr4:4p16.3-q35.2
pathogenic
NM_001134665.3(TRMT10A):c.172C>A (p.Arg58=) single nucleotide variant not provided [RCV000880431] Chr4:99559167 [GRCh38]
Chr4:100480324 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.665C>T (p.Ala222Val) single nucleotide variant not provided [RCV000893907]|not specified [RCV001818692] Chr4:99550971 [GRCh38]
Chr4:100472128 [GRCh37]
Chr4:4q23
likely benign|uncertain significance
NM_001134665.3(TRMT10A):c.888G>A (p.Arg296=) single nucleotide variant not provided [RCV000980093] Chr4:99549220 [GRCh38]
Chr4:100470377 [GRCh37]
Chr4:4q23
likely benign
GRCh37/hg19 4q23(chr4:100239111-100509321)x3 copy number gain not provided [RCV000847681] Chr4:100239111..100509321 [GRCh37]
Chr4:4q23
uncertain significance
GRCh37/hg19 4q23(chr4:100224894-100482676)x3 copy number gain not provided [RCV000849380] Chr4:100224894..100482676 [GRCh37]
Chr4:4q23
uncertain significance
GRCh37/hg19 4q23(chr4:100224894-100482676)x3 copy number gain not provided [RCV000849382] Chr4:100224894..100482676 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.348G>C (p.Lys116Asn) single nucleotide variant Microcephaly, short stature, and impaired glucose metabolism 1 [RCV001264827] Chr4:99558049 [GRCh38]
Chr4:100479206 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.697_698delinsTA (p.Pro233Ter) indel Microcephaly, short stature, and impaired glucose metabolism 1 [RCV001251196] Chr4:99550938..99550939 [GRCh38]
Chr4:100472095..100472096 [GRCh37]
Chr4:4q23
likely pathogenic
GRCh37/hg19 4q22.2-24(chr4:94692345-101308220)x1 copy number loss not provided [RCV001259285] Chr4:94692345..101308220 [GRCh37]
Chr4:4q22.2-24
likely pathogenic
NM_001134665.3(TRMT10A):c.388G>A (p.Ala130Thr) single nucleotide variant Microcephaly, short stature, and impaired glucose metabolism 1 [RCV001330415] Chr4:99557377 [GRCh38]
Chr4:100478534 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.388G>T (p.Ala130Ser) single nucleotide variant Microcephaly, short stature, and impaired glucose metabolism 1 [RCV001330416] Chr4:99557377 [GRCh38]
Chr4:100478534 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.277C>T (p.Arg93Ter) single nucleotide variant Abnormality of the nervous system [RCV001814306] Chr4:99558120 [GRCh38]
Chr4:100479277 [GRCh37]
Chr4:4q23
pathogenic|likely pathogenic
NM_001134665.3(TRMT10A):c.186-10C>T single nucleotide variant not provided [RCV001522088] Chr4:99558221 [GRCh38]
Chr4:100479378 [GRCh37]
Chr4:4q23
benign
NM_001134665.3(TRMT10A):c.465T>A (p.Asp155Glu) single nucleotide variant not specified [RCV001817452] Chr4:99556176 [GRCh38]
Chr4:100477333 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.23dup (p.Phe9fs) duplication Microcephaly, short stature, and impaired glucose metabolism 1 [RCV001806433] Chr4:99559315..99559316 [GRCh38]
Chr4:100480472..100480473 [GRCh37]
Chr4:4q23
pathogenic
NM_001134665.3(TRMT10A):c.149A>T (p.Lys50Ile) single nucleotide variant not provided [RCV001869652]|not specified [RCV001822191] Chr4:99559190 [GRCh38]
Chr4:100480347 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.934A>G (p.Ser312Gly) single nucleotide variant not provided [RCV001869767]|not specified [RCV001822658] Chr4:99549174 [GRCh38]
Chr4:100470331 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.78G>C (p.Glu26Asp) single nucleotide variant not specified [RCV001819549] Chr4:99559261 [GRCh38]
Chr4:100480418 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.854G>A (p.Cys285Tyr) single nucleotide variant not specified [RCV001820718] Chr4:99549254 [GRCh38]
Chr4:100470411 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.727C>T (p.Arg243Ter) single nucleotide variant not provided [RCV001984789] Chr4:99550909 [GRCh38]
Chr4:100472066 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.337A>G (p.Met113Val) single nucleotide variant not provided [RCV001950594] Chr4:99558060 [GRCh38]
Chr4:100479217 [GRCh37]
Chr4:4q23
uncertain significance
GRCh37/hg19 4q12-31.21(chr4:52866944-143582507)x3 copy number gain not provided [RCV001827738] Chr4:52866944..143582507 [GRCh37]
Chr4:4q12-31.21
pathogenic
NM_001134665.3(TRMT10A):c.215A>G (p.Lys72Arg) single nucleotide variant not provided [RCV001927774] Chr4:99558182 [GRCh38]
Chr4:100479339 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.823C>A (p.Arg275=) single nucleotide variant not provided [RCV002005142] Chr4:99549285 [GRCh38]
Chr4:100470442 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.438C>G (p.His146Gln) single nucleotide variant not provided [RCV001913604] Chr4:99556203 [GRCh38]
Chr4:100477360 [GRCh37]
Chr4:4q23
uncertain significance
GRCh37/hg19 4q22.3-25(chr4:95490755-109977216)x3 copy number gain not provided [RCV001827745] Chr4:95490755..109977216 [GRCh37]
Chr4:4q22.3-25
likely pathogenic
NM_001134665.3(TRMT10A):c.569C>T (p.Ser190Leu) single nucleotide variant not provided [RCV001895145] Chr4:99553861 [GRCh38]
Chr4:100475018 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.899G>A (p.Gly300Asp) single nucleotide variant not provided [RCV001969715] Chr4:99549209 [GRCh38]
Chr4:100470366 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.193C>T (p.Arg65Ter) single nucleotide variant not provided [RCV001941776] Chr4:99558204 [GRCh38]
Chr4:100479361 [GRCh37]
Chr4:4q23
pathogenic
NC_000004.11:g.(?_100470245)_(100521910_?)dup duplication not provided [RCV001943284] Chr4:100470245..100521910 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.205C>T (p.Arg69Cys) single nucleotide variant not provided [RCV002028075] Chr4:99558192 [GRCh38]
Chr4:100479349 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.495+2T>C single nucleotide variant not provided [RCV002046680] Chr4:99556144 [GRCh38]
Chr4:100477301 [GRCh37]
Chr4:4q23
likely pathogenic
NM_001134665.3(TRMT10A):c.227G>A (p.Arg76Gln) single nucleotide variant not provided [RCV001864768] Chr4:99558170 [GRCh38]
Chr4:100479327 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.206G>T (p.Arg69Leu) single nucleotide variant not provided [RCV001952819] Chr4:99558191 [GRCh38]
Chr4:100479348 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.683A>G (p.Asn228Ser) single nucleotide variant not provided [RCV001998484] Chr4:99550953 [GRCh38]
Chr4:100472110 [GRCh37]
Chr4:4q23
uncertain significance
NC_000004.11:g.(?_100239320)_(100544005_?)dup duplication not provided [RCV002018710] Chr4:100239320..100544005 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.305G>A (p.Arg102His) single nucleotide variant not provided [RCV001996793] Chr4:99558092 [GRCh38]
Chr4:100479249 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.380G>A (p.Arg127Gln) single nucleotide variant not provided [RCV001989942] Chr4:99557385 [GRCh38]
Chr4:100478542 [GRCh37]
Chr4:4q23
uncertain significance
NM_001134665.3(TRMT10A):c.349-18A>T single nucleotide variant not provided [RCV002085782] Chr4:99557434 [GRCh38]
Chr4:100478591 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.349-17dup duplication not provided [RCV002168754] Chr4:99557432..99557433 [GRCh38]
Chr4:100478589..100478590 [GRCh37]
Chr4:4q23
benign
NM_001134665.3(TRMT10A):c.366T>C (p.His122=) single nucleotide variant not provided [RCV002075856] Chr4:99557399 [GRCh38]
Chr4:100478556 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.438C>T (p.His146=) single nucleotide variant not provided [RCV002091000] Chr4:99556203 [GRCh38]
Chr4:100477360 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.159A>G (p.Gln53=) single nucleotide variant not provided [RCV002112953] Chr4:99559180 [GRCh38]
Chr4:100480337 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.752-20G>A single nucleotide variant not provided [RCV002212462] Chr4:99549376 [GRCh38]
Chr4:100470533 [GRCh37]
Chr4:4q23
benign
NM_001134665.3(TRMT10A):c.45T>C (p.Val15=) single nucleotide variant not provided [RCV002074785] Chr4:99559294 [GRCh38]
Chr4:100480451 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.561G>A (p.Thr187=) single nucleotide variant not provided [RCV002151892] Chr4:99553869 [GRCh38]
Chr4:100475026 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.696C>A (p.Leu232=) single nucleotide variant not provided [RCV002142694] Chr4:99550940 [GRCh38]
Chr4:100472097 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.978G>A (p.Lys326=) single nucleotide variant not provided [RCV002199463] Chr4:99549130 [GRCh38]
Chr4:100470287 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.495+11_495+54del deletion not provided [RCV002143515] Chr4:99556092..99556135 [GRCh38]
Chr4:100477249..100477292 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.273T>G (p.Arg91=) single nucleotide variant not provided [RCV002162277] Chr4:99558124 [GRCh38]
Chr4:100479281 [GRCh37]
Chr4:4q23
likely benign
NM_001134665.3(TRMT10A):c.408G>A (p.Leu136=) single nucleotide variant not provided [RCV002199630] Chr4:99557357 [GRCh38]
Chr4:100478514 [GRCh37]
Chr4:4q23
likely benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:28403 AgrOrtholog
COSMIC TRMT10A COSMIC
Ensembl Genes ENSG00000145331 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000273962 ENTREZGENE
  ENSP00000273962.3 UniProtKB/Swiss-Prot
  ENSP00000378342 ENTREZGENE
  ENSP00000378342.2 UniProtKB/Swiss-Prot
  ENSP00000378343 ENTREZGENE
  ENSP00000378343.3 UniProtKB/Swiss-Prot
  ENSP00000397551.2 UniProtKB/TrEMBL
  ENSP00000423628.1 UniProtKB/TrEMBL
Ensembl Transcript ENST00000273962 ENTREZGENE
  ENST00000273962.7 UniProtKB/Swiss-Prot
  ENST00000394876 ENTREZGENE
  ENST00000394876.7 UniProtKB/Swiss-Prot
  ENST00000394877 ENTREZGENE
  ENST00000394877.7 UniProtKB/Swiss-Prot
  ENST00000455368.6 UniProtKB/TrEMBL
  ENST00000514547.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.1280.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000145331 GTEx
HGNC ID HGNC:28403 ENTREZGENE
Human Proteome Map TRMT10A Human Proteome Map
InterPro MT_TRM10-typ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MT_TRM10-typ_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRM10/TRM10A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  tRNA_m1G_MeTrfase_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  tRNA_MeTrfase_TRMD/TRM10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:93587 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 93587 ENTREZGENE
OMIM 616013 OMIM
  616033 OMIM
PANTHER PTHR13563 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13563:SF13 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam tRNA_m1G_MT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134979919 PharmGKB
PIRSF tRNA_m1G_mtfrase_met UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SAM_MT_TRM10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt D6R954_HUMAN UniProtKB/TrEMBL
  Q8TBZ6 ENTREZGENE, UniProtKB/Swiss-Prot
  V9HVY8 ENTREZGENE, UniProtKB/TrEMBL
  X6REK4_HUMAN UniProtKB/TrEMBL
UniProt Secondary A0A024RDJ9 UniProtKB/TrEMBL
  B2R8X7 UniProtKB/Swiss-Prot
  Q9Y2T9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-09-29 TRMT10A  tRNA methyltransferase 10A    tRNA methyltransferase 10 homolog A (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED
2012-07-05 TRMT10A  tRNA methyltransferase 10 homolog A (S. cerevisiae)  RG9MTD2  RNA (guanine-9-) methyltransferase domain containing 2  Symbol and/or name change 5135510 APPROVED