MT-TS2 (mitochondrially encoded tRNA-Ser (AGU/C) 2) - Rat Genome Database

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Gene: MT-TS2 (mitochondrially encoded tRNA-Ser (AGU/C) 2) Homo sapiens
Analyze
Symbol: MT-TS2
Name: mitochondrially encoded tRNA-Ser (AGU/C) 2
RGD ID: 1344420
HGNC Page HGNC:7498
Description: ASSOCIATED WITH Abnormal central motor function; Abnormal cochlea morphology; Abnormal electroretinogram; INTERACTS WITH bisphenol A; lipopolysaccharide
Type: trna (Ensembl: Mt_tRNA)
Previously known as: mitochondrially encoded tRNA serine 2 (AGU/C); MTTS2; retinitis pigmentosa 21; RP21
RGD Orthologs
Mouse
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
GRCh38MT12,207 - 12,265 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblMT12,207 - 12,265 (+)EnsemblGRCh38hg38GRCh38
GRCh37MT12,207 - 12,265 (+)NCBIGRCh37GRCh37hg19GRCh37


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Abnormal central motor function  (IAGP)
Abnormal cochlea morphology  (IAGP)
Abnormal electroretinogram  (IAGP)
Abnormal left ventricular function  (IAGP)
Abnormal mitochondria in muscle tissue  (IAGP)
Abnormality of movement  (IAGP)
Agenesis of corpus callosum  (IAGP)
Anemia  (IAGP)
Anxiety  (IAGP)
Aphasia  (IAGP)
Aplasia/Hypoplasia of the cerebral white matter  (IAGP)
Arrhythmia  (IAGP)
Astigmatism  (IAGP)
Ataxia  (IAGP)
Basal ganglia calcification  (IAGP)
Bilateral cleft lip and palate  (IAGP)
Bilateral sensorineural hearing impairment  (IAGP)
Bilateral tonic-clonic seizure  (IAGP)
Bipolar affective disorder  (IAGP)
Brain atrophy  (IAGP)
Camptodactyly of finger  (IAGP)
Cardiac conduction abnormality  (IAGP)
Cardiomyopathy  (IAGP)
Cataract  (IAGP)
Cerebral cortical atrophy  (IAGP)
Cerebral visual impairment  (IAGP)
Cognitive impairment  (IAGP)
Concentric hypertrophic cardiomyopathy  (IAGP)
Cone/cone-rod dystrophy  (IAGP)
Congestive heart failure  (IAGP)
Constipation  (IAGP)
Dementia  (IAGP)
Depression  (IAGP)
Developmental cataract  (IAGP)
Diabetes mellitus  (IAGP)
Diarrhea  (IAGP)
Dilated cardiomyopathy  (IAGP)
Distal peripheral sensory neuropathy  (IAGP)
EEG abnormality  (IAGP)
Elevated brain lactate level by MRS  (IAGP)
EMG abnormality  (IAGP)
Encephalopathy  (IAGP)
Episodic vomiting  (IAGP)
Erythema  (IAGP)
Exercise intolerance  (IAGP)
Failure to thrive  (IAGP)
Fever  (IAGP)
Fluctuations in consciousness  (IAGP)
Focal segmental glomerulosclerosis  (IAGP)
Focal-onset seizure  (IAGP)
Gait disturbance  (IAGP)
Gastrointestinal dysmotility  (IAGP)
Generalized myoclonic seizure  (IAGP)
Global developmental delay  (IAGP)
Growth abnormality  (IAGP)
Hallucinations  (IAGP)
Hemianopia  (IAGP)
Hemiparesis  (IAGP)
High hypermetropia  (IAGP)
Hypertelorism  (IAGP)
Hypertension  (IAGP)
Hypertrichosis  (IAGP)
Hypertrophic cardiomyopathy  (IAGP)
Hypogonadotropic hypogonadism  (IAGP)
Hypoparathyroidism  (IAGP)
Hypoplasia of the corpus callosum  (IAGP)
Hypothyroidism  (IAGP)
Impaired visuospatial constructive cognition  (IAGP)
Increased circulating lactate concentration  (IAGP)
Increased CSF lactate  (IAGP)
Increased CSF protein concentration  (IAGP)
Intestinal pseudo-obstruction  (IAGP)
Iris hypopigmentation  (IAGP)
Lactic acidosis  (IAGP)
Leber optic atrophy  (IAGP)
Left ventricular hypertrophy  (IAGP)
Low-set ears  (IAGP)
Macrocytic dyserythropoietic anemia  (IAGP)
Memory impairment  (IAGP)
Migraine  (IAGP)
Mitochondrial inheritance  (IAGP)
Mitochondrial myopathy  (IAGP)
Mixed demyelinating and axonal polyneuropathy  (IAGP)
Motor delay  (IAGP)
Multiple lipomas  (IAGP)
Muscle weakness  (IAGP)
Myoclonus  (IAGP)
Myopathy  (IAGP)
Nephropathy  (IAGP)
Nyctalopia  (IAGP)
Ophthalmoplegia  (IAGP)
Optic atrophy  (IAGP)
Peripheral axonal neuropathy  (IAGP)
Peripheral neuropathy  (IAGP)
Personality changes  (IAGP)
Pigmentary retinopathy  (IAGP)
Postaxial hand polydactyly  (IAGP)
Premature birth  (IAGP)
Progressive external ophthalmoplegia  (IAGP)
Progressive sensorineural hearing impairment  (IAGP)
Proteinuria  (IAGP)
Proximal tubulopathy  (IAGP)
Psychosis  (IAGP)
Psychotic mentation  (IAGP)
Pulmonary arterial hypertension  (IAGP)
Ragged-red muscle fibers  (IAGP)
Recurrent pancreatitis  (IAGP)
Recurrent paroxysmal headache  (IAGP)
Reduced consciousness  (IAGP)
Rod-cone dystrophy  (IAGP)
Schizophrenia  (IAGP)
Scotoma  (IAGP)
Seizure  (IAGP)
Sensorimotor neuropathy  (IAGP)
Sensorineural hearing impairment  (IAGP)
Short attention span  (IAGP)
Short stature  (IAGP)
Specific learning disability  (IAGP)
Stroke-like episode  (IAGP)
Stuttering  (IAGP)
Type I diabetes mellitus  (IAGP)
Type II diabetes mellitus  (IAGP)
Variable expressivity  (IAGP)
Vestibular hypofunction  (IAGP)
Visual loss  (IAGP)
Vitiligo  (IAGP)
Vomiting  (IAGP)
Wide intermamillary distance  (IAGP)
Widened cerebral subarachnoid space  (IAGP)
Wolff-Parkinson-White syndrome  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. RGD HPO Phenotype Annotation Pipeline RGD automated import pipeline for human HPO-to-gene-to-disease annotations
Additional References at PubMed
PMID:RP21   PMID:12045211   PMID:19758471   PMID:20301403   PMID:20301411   PMID:22378285  


Genomics

Comparative Map Data
MT-TS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38MT12,207 - 12,265 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblMT12,207 - 12,265 (+)EnsemblGRCh38hg38GRCh38
GRCh37MT12,207 - 12,265 (+)NCBIGRCh37GRCh37hg19GRCh37
mt-Ts2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39MT11,613 - 11,671 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblMT11,613 - 11,671 (+)EnsemblGRCm39 Ensembl
GRCm38MT11,613 - 11,671 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblMT11,613 - 11,671 (+)EnsemblGRCm38mm10GRCm38
MGSCv37MT11,613 - 11,671 (+)NCBIGRCm37MGSCv37mm9NCBIm37

Variants

.
Variants in MT-TS2
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
m.12258C>A single nucleotide variant Cerebellar ataxia, cataract, and diabetes mellitus [RCV000010170]|Mitochondrial disease [RCV003162227]|Retinitis pigmentosa-deafness syndrome [RCV000010171] ChrMT:12258 [GRCh38]
ChrMT:12258 [GRCh37]
pathogenic|likely pathogenic
m.12207G>A AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV002247285]|MERRF/MELAS overlap syndrome [RCV000010173] ChrMT:12207 [GRCh38]
ChrMT:12207 [GRCh37]
pathogenic
NC_012920.1:m.5782_13922del8141 deletion Primary dilated cardiomyopathy [RCV000191151] ChrMT:5782..13922 [GRCh38]
ChrMT:5782..13922 [GRCh37]
likely pathogenic
NC_012920.1:m.5794_14876del9083 deletion Primary dilated cardiomyopathy [RCV000191152] ChrMT:5794..14876 [GRCh38]
ChrMT:5794..14876 [GRCh37]
likely pathogenic
NC_012920.1(MT-CYB):m.12239C>T single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851055]|Mitochondrial disease [RCV002221520]|not provided [RCV000224786] ChrMT:12239 [GRCh38]
ChrMT:12239 [GRCh37]
pathogenic|benign
NC_012920.1(MT-TS2):m.12236G>A single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851053]|not provided [RCV000992385]|not specified [RCV000506174] ChrMT:12236 [GRCh38]
ChrMT:12236 [GRCh37]
benign|uncertain significance
NC_012920.1:m.8483_13459del4977 deletion Kearns-Sayre syndrome [RCV000855712]|Mitochondrial disease [RCV000495046] ChrMT:8470..13446 [GRCh38]
ChrMT:8470..13446 [GRCh37]
pathogenic|not provided
NC_012920.1:m.8815_13722del4908 deletion Mitochondrial disease [RCV000494750] ChrMT:8815..13722 [GRCh38]
ChrMT:8815..13722 [GRCh37]
pathogenic
NC_012920.1:m.11263_15374del4112 deletion Mitochondrial disease [RCV000494855] ChrMT:11263..15374 [GRCh38]
ChrMT:11263..15374 [GRCh37]
pathogenic
NC_012920.1:m.8839_14895del6057 deletion Mitochondrial disease [RCV000495147] ChrMT:8839..14895 [GRCh38]
ChrMT:8839..14895 [GRCh37]
pathogenic
NC_012920.1:m.12114_14420del2307 deletion Mitochondrial disease [RCV000495253] ChrMT:12114..14420 [GRCh38]
ChrMT:12114..14420 [GRCh37]
pathogenic
NC_012920.1:m.6469_15587del9119 deletion Mitochondrial disease [RCV000495334] ChrMT:6468..15586 [GRCh38]
ChrMT:6468..15586 [GRCh37]
pathogenic
NC_012920.1:m.8587_12967del4381 deletion Mitochondrial disease [RCV000495437] ChrMT:8585..12965 [GRCh38]
ChrMT:8585..12965 [GRCh37]
pathogenic
NC_012920.1:m.8290_13040del4751 deletion Mitochondrial disease [RCV000495493] ChrMT:8290..13040 [GRCh38]
ChrMT:8290..13040 [GRCh37]
pathogenic
NC_012920.1:m.10106_15067del4962 deletion Mitochondrial disease [RCV000495541] ChrMT:10105..15066 [GRCh38]
ChrMT:10105..15066 [GRCh37]
pathogenic
NC_012920.1:m.7129_13991del6863 deletion Mitochondrial disease [RCV000495692] ChrMT:7126..13988 [GRCh38]
ChrMT:7126..13988 [GRCh37]
pathogenic|likely pathogenic
NC_012920.1:m.8350_13450del deletion Pearson syndrome [RCV000790615] ChrMT:8350..13450 [GRCh38]
ChrMT:8350..13450 [GRCh37]
pathogenic
NC_012920.1(MT-CYB):m.12217A>G single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851046]|not provided [RCV001288304] ChrMT:12217 [GRCh38]
ChrMT:12217 [GRCh37]
benign|uncertain significance
NC_012920.1(MT-CYB):m.12223A>G AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851048] ChrMT:12223 [GRCh38]
ChrMT:12223 [GRCh37]
benign
NC_012920.1(MT-CYB):m.12237C>T AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851054] ChrMT:12237 [GRCh38]
ChrMT:12237 [GRCh37]
benign
NC_012920.1(MT-CYB):m.12241del deletion Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851056]|See cases [RCV001250990] ChrMT:12237 [GRCh38]
ChrMT:12237 [GRCh37]
benign|uncertain significance
NC_012920.1(MT-CYB):m.12241dup AND Juvenile myopathy, encephalopathy, lactic acidosis duplication Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851057] ChrMT:12236..12237 [GRCh38]
ChrMT:12236..12237 [GRCh37]
uncertain significance
NC_012920.1(MT-CYB):m.12245T>C AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851058] ChrMT:12245 [GRCh38]
ChrMT:12245 [GRCh37]
benign
NC_012920.1:m.8480_13440del deletion Pearson syndrome [RCV000790614] ChrMT:8480..13440 [GRCh38]
ChrMT:8480..13440 [GRCh37]
pathogenic
NC_012920.1(MT-CYB):m.12234A>G AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851051] ChrMT:12234 [GRCh38]
ChrMT:12234 [GRCh37]
benign
NC_012920.1(MT-CYB):m.12235T>C AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851052] ChrMT:12235 [GRCh38]
ChrMT:12235 [GRCh37]
benign
NC_012920.1(MT-CYB):m.12247T>C AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851060] ChrMT:12247 [GRCh38]
ChrMT:12247 [GRCh37]
uncertain significance
NC_012920.1(MT-CYB):m.12250C>T AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851062] ChrMT:12250 [GRCh38]
ChrMT:12250 [GRCh37]
uncertain significance
NC_012920.1(MT-CYB):m.12264C>T AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851065] ChrMT:12264 [GRCh38]
ChrMT:12264 [GRCh37]
pathogenic|likely pathogenic
NC_012920.1(MT-CYB):m.12216C>T AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851045] ChrMT:12216 [GRCh38]
ChrMT:12216 [GRCh37]
benign
NC_012920.1(MT-CYB):m.12218C>A AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851047] ChrMT:12218 [GRCh38]
ChrMT:12218 [GRCh37]
uncertain significance
NC_012920.1(MT-CYB):m.12230A>G AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851049] ChrMT:12230 [GRCh38]
ChrMT:12230 [GRCh37]
uncertain significance
NC_012920.1(MT-CYB):m.12231C>T AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851050] ChrMT:12231 [GRCh38]
ChrMT:12231 [GRCh37]
likely benign
NC_012920.1(MT-CYB):m.12248A>G AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851061] ChrMT:12248 [GRCh38]
ChrMT:12248 [GRCh37]
benign
NC_012920.1(MT-CYB):m.12213G>A AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851043] ChrMT:12213 [GRCh38]
ChrMT:12213 [GRCh37]
uncertain significance
NC_012920.1(MT-CYB):m.12215T>C AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851044] ChrMT:12215 [GRCh38]
ChrMT:12215 [GRCh37]
benign
NC_012920.1(MT-CYB):m.12258C>T AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851064] ChrMT:12258 [GRCh38]
ChrMT:12258 [GRCh37]
pathogenic|likely pathogenic
NC_012920.1(MT-CYB):m.12265A>G AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851066] ChrMT:12265 [GRCh38]
ChrMT:12265 [GRCh37]
likely benign
NC_012920.1(MT-CYB):m.12246C>T AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851059] ChrMT:12246 [GRCh38]
ChrMT:12246 [GRCh37]
benign
NC_012920.1(MT-CYB):m.12255T>C AND Juvenile myopathy, encephalopathy, lactic acidosis single nucleotide variant Juvenile myopathy, encephalopathy, lactic acidosis AND stroke [RCV000851063] ChrMT:12255 [GRCh38]
ChrMT:12255 [GRCh37]
uncertain significance
NC_012920.1(MT-TS2):m.12246C>A single nucleotide variant not specified [RCV002248017] ChrMT:12246 [GRCh38]
ChrMT:12246 [GRCh37]
uncertain significance
Single allele deletion Pearson syndrome [RCV003223355] ChrMT:10947..15537 [GRCh38]
ChrMT:10947..15537 [GRCh37]
pathogenic
NC_012920.1:m.8993T>G single nucleotide variant Cerebellar ataxia [RCV000191106]|Hypertelorism [RCV000414771]|Leber optic atrophy [RCV001542706]|Leigh syndrome [RCV000010273]|Mitochondrial complex 5 (ATP synthase) deficiency, mitochondrial type 1 [RCV000754646]|Mitochondrial disease [RCV000495419]|NARP syndrome [RCV000010274]|Rod-cone dystrophy [RCV001376274]|not provided [RCV000224643]|not specified [RCV002285006] ChrMT:8993 [GRCh38]
ChrMT:8993 [GRCh37]
pathogenic|likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:174
Count of miRNA genes:168
Interacting mature miRNAs:173
Transcripts:ENST00000387449
Prediction methods: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 adipose tissue appendage
High 2
Medium 55 43 59 22 375 17 65 55 147 46 29 49 5 23 40
Low 1265 1182 793 233 378 186 1620 1245 2537 175 476 544 47 583 1044
Below cutoff 64 102 40 26 44 18 144 128 67 8 20 16 8 36 112

Sequence

Nucleotide Sequences

RefSeq Acc Id: ENST00000387449
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 EnsemblMT12,207 - 12,265 (+)Ensembl

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:7498 AgrOrtholog
COSMIC MT-TS2 COSMIC
Ensembl Genes ENSG00000210184 Ensembl
GTEx ENSG00000210184 GTEx
HGNC ID HGNC:7498 ENTREZGENE
Human Proteome Map MT-TS2 Human Proteome Map
NCBI Gene MT-TS2 ENTREZGENE
OMIM 590085 OMIM
PharmGKB PA31301 PharmGKB


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-02-26 MT-TS2  mitochondrially encoded tRNA-Ser (AGU/C) 2  MT-TS2  mitochondrially encoded tRNA serine 2 (AGU/C)  Symbol and/or name change 19259463 PROVISIONAL
2016-04-06 MT-TS2  mitochondrially encoded tRNA serine 2 (AGU/C)  RP21  retinitis pigmentosa 21  Data merged from RGD:1346565 737654 PROVISIONAL
2015-05-19 MT-TS2  mitochondrially encoded tRNA serine 2 (AGU/C)  TRNS2  mitochondrially encoded tRNA serine 2 (AGU/C)  Symbol and/or name change 5135510 APPROVED
2015-05-19 MT-TS2  mitochondrially encoded tRNA serine 2 (AGU/C)  TRNS2    Symbol and/or name change 5135510 APPROVED
2014-01-07 TRNS2  mitochondrially encoded tRNA serine 2 (AGU/C)  MT-TS2  mitochondrially encoded tRNA serine 2 (AGU/C)  Symbol and/or name change 5135510 APPROVED
2014-01-07 TRNS2  mitochondrially encoded tRNA serine 2 (AGU/C)  MT-TS2    Symbol and/or name change 5135510 APPROVED