MT-RNR1

Summary

MT-RNR1 (mitochondrially encoded 12S rRNA, HGNC:7470) is a mitochondrial rRNA gene on chromosome mitochondria. Regulates insulin sensitivity and metabolic homeostasis.

Enables DNA binding activity and DNA-binding transcription factor binding activity. Involved in several processes, including osteoblast proliferation; regulation of carbohydrate utilization; and regulation of phosphate metabolic process. Located in extracellular space; mitochondrion; and nucleus.

Source: NCBI Gene 4549 — RefSeq curated summary.

At a glance

• Gene type: non-coding (Mt_rRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7470
Approved symbol	MT-RNR1
Name	mitochondrially encoded 12S rRNA
Location	mitochondria
Locus type	RNA, ribosomal
Status	Approved
Aliases	12S, MOTS-c
Ensembl gene	ENSG00000211459
Ensembl biotype	Mt_rRNA
OMIM	561000
Entrez	4549
RNAcentral	URS000044DFF6 — ncRNA, 954 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 Mt_rRNA

ENST00000389680

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000389680 — 1 exons

Exon	Start	End
ENSE00001544499	648	1601

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 100.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 283.0681 / max 6970.8726, expressed in 1799 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
194816	283.0681	1799

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	100.00	gold quality
monocyte	CL:0000576	99.99	gold quality
prefrontal cortex	UBERON:0000451	99.99	gold quality
adrenal tissue	UBERON:0018303	99.99	gold quality
leukocyte	CL:0000738	99.98	gold quality
frontal cortex	UBERON:0001870	99.98	gold quality
temporal lobe	UBERON:0001871	99.98	gold quality
caudate nucleus	UBERON:0001873	99.98	gold quality
putamen	UBERON:0001874	99.98	gold quality
amygdala	UBERON:0001876	99.98	gold quality
nucleus accumbens	UBERON:0001882	99.98	gold quality
hypothalamus	UBERON:0001898	99.98	gold quality
Ammon’s horn	UBERON:0001954	99.98	gold quality
substantia nigra	UBERON:0002038	99.98	gold quality
hindlimb stylopod muscle	UBERON:0004252	99.98	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	99.98	gold quality
Brodmann (1909) area 9	UBERON:0013540	99.98	gold quality
adult mammalian kidney	UBERON:0000082	99.97	gold quality
cerebral cortex	UBERON:0000956	99.97	gold quality
cortex of kidney	UBERON:0001225	99.97	gold quality
cerebellum	UBERON:0002037	99.97	gold quality
cerebellar cortex	UBERON:0002129	99.97	gold quality
cerebellar hemisphere	UBERON:0002245	99.97	gold quality
primary visual cortex	UBERON:0002436	99.97	gold quality
superior frontal gyrus	UBERON:0002661	99.97	gold quality
right frontal lobe	UBERON:0002810	99.97	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	99.97	gold quality
anterior cingulate cortex	UBERON:0009835	99.97	gold quality
metanephros cortex	UBERON:0010533	99.97	gold quality
right hemisphere of cerebellum	UBERON:0014890	99.97	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-MTAB-10662	yes	32743.32
E-MTAB-10287	yes	25610.37
E-GEOD-180759	yes	24831.37
E-GEOD-131882	yes	19602.47
E-CURD-126	yes	8481.06
E-HCAD-35	yes	4505.16
E-MTAB-9543	no	31021.87
E-CURD-119	no	23953.34
E-HCAD-30	no	9414.87
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 40)

• mutation resulted in aminoglycoside-induced deafness (PMID:11870684)
• T1391C mutation in the 12S ribosomal RNA gene: importance in disease expression remains to be clarified. (PMID:12031626)
• Mitochondrial 12S rRNA A1555G mutation is a significant cause of prelingual non-syndromic deafness in the Turkish population (PMID:12655418)
• Poorly differentiated gastric cancers are more prone to 12S rRNA-tRNA(phe) variations, or gastric cancers with 12S rRNA-tRNA(phe) variations are more likely to be poorly differentiated. (PMID:12970877)
• The pathogenetic mechanism of the deafness-associated mitochondrial 12S rRNA C1494T mutation was investigated. (PMID:15722487)
• The occurrence of the A827G mutation in genetically unrelated subjects strongly suggests that this mutation is involved in the pathogenesis of hearing impairment. (PMID:16650816)
• Variants in mitochondrial tRNAGlu, tRNAArg, and tRNAThr may influence the phenotypic manifestation of deafness-associated 12S rRNA A1555G mutation in three Han Chinese families with hearing loss. (PMID:16955413)
• There was a high proportion of hereditary hearing impairment caused by mtDNA 12SrRNA A1555G mutation in 5 provinces of northwest region of China. (PMID:17650818)
• Maternally inherited aminoglycoside-induced and nonsyndromic hearing loss is associated with the 12S rRNA C1494T mutation in three Han Chinese pedigrees. (PMID:17698299)
• Then HaeIII polymorphic restriction site in the gene of 12S rRNA site was found in 4 out of 100 patients with non-syndromic hearing loss. (PMID:18325329)
• mitochondrial 12S/MT-RNR1, MT-CO2/COX2, and MT-ATP6 transcripts is significantly decreased in prostates tumor samples (PMID:18409190)
• They did not identify any mitochondrial 12S rRNA mutation of proven pathogenicity in the collection of aminoglycoside-associated and idiopathic bilateral vestibulopathy patients. (PMID:18851951)
• Mitochondrial tRNA(Glu) variant modulate the phenotype of deafness-associated 12S rRNA A1555G mutation in Chinese family. (PMID:19376484)
• These results indicated that the A1555G mutation in the mitochondrial 12S ribosomal RNA gene can cause vestibular dysfunction, especially saccular dysfunction and cochlear dysfunction. (PMID:19536740)
• Mitochondrial 12S rRNA G709A mutation was associated with non-syndromic inherited hearing loss. (PMID:19953480)
• data demonstrated that mitochondrial 12S rRNA is the hot spot for mutations associated with aminoglycoside ototoxicity (PMID:20100600)
• mutational screening of the entire mitochondrial 12S rRNA gene was performed to estimate the involvement and the frequency of known and putative mutations in Polish patients with non-syndromic and aminoglycoside-induced hearing loss. (PMID:20353758)
• The prevalence of 12S rRNA mutations related to aminoglycoside ototoxicity in our study population was approximately one percent. (PMID:20416460)
• Large-scale screening of mitochondrial DNA m.1555A>G mutation in 2417 deaf-mute students in northwest of China. (PMID:20662562)
• The incidence of mtDNA A1555G in Uigur patients is lower than the average level of the overall Chinese deaf population. (PMID:20669656)
• The T1095C mutation in 12S rRNA is correlated with military noise induced-hearing loss. (PMID:20669660)
• The m.827A>G sequence variant was found in both deaf and normal subjects and is unlikely to have a pathogenic role in hereditary deafness. (PMID:20722495)
• In Xinjiang, the mtDNA 12SRNA A1555G mutation rate was high in Uighur and Han people with hereditary nonsyndromic hearing loss (PMID:21055240)
• single variant that may be pathogenic found (PMID:21114417)
• The mitochondrial 12S rRNA is the hot spot for mutations associated with aminoglycoside ototoxicity. (PMID:21205314)
• Mutational screening of the mitochondrial 12S rRNA gene in Polish patients with aminoglycoside-induced hearing loss (PMID:22000150)
• Novel mutations in the MT-RNR1 gene that affected secondary structure were identified in nonsyndromic hearing loss patients. (PMID:22852811)
• Report mitochondrial 12S rRNA 1494C> T mutation as responsible for aminoglycoside-induced and non-syndromic hearing loss. (PMID:23237192)
• We suggested the variation of two nucleotides 1245 and 1545 that localized at conserved site of 12SrRNA may be new candidate for amino glycoside-induced and nonsyndromic hearing impairment associated mutations. (PMID:23242658)
• Mitochondrial 12S rRNA A1555G mutation is associated with nonsyndromic hearing loss Han Chinese pedigrees. (PMID:23357266)
• mtDNA A1555G mutation was detected in six Tibetan, five Tu nationality, and one Mongolian subject; one Tibetan patient carried the C1494T mutation. (PMID:23834103)
• study analyzed 5 heteroplasmy pedigrees with hearing loss and the A1555G mutation; results suggest large random shifts in heteroplasmy level between mothers and offspring with the A1555G mutation; heteroplasmy level may be one of the factors influencing penetrance of deafness caused by the mtDNA A1555G mutation (PMID:24533451)
• Differential expression of mutation m.1555A>G of the mitochondrial MT-RNR1 gene in a South Indian family with postlingual hearing loss. (PMID:24660976)
• The prevalence of mtDNA 12S rRNA A1555G homozygous mutations was 6.05%, 3.27%, and 1.44% in Han Chinese, Hui people, and Uyghur participants (chi(2) = 13.9, P < 0.05), respectively (PMID:24804242)
• Contribution of GJB2, SLC26A4, and MTRNR1 mutations to Mild-to-Moderate childhood hearing impairment in Chinese Hans. (PMID:25251670)
• Mutations in 12S rRNA, SLC26A4, GJB2 and GJB3 are highly associated with deafness. (PMID:26037344)
• exon sequencing of GJB2, SLC26A4, and mtDNA12SrRNA reveals that non-syndromic deafness in Xiamen, China appears to have a genetic etiology (PMID:26252218)
• Data show methylation status of two mitochondrial genes MT-RNR1 and MT-RNR2 encoding for mitochondrial 12S and 16S ribosomal RNAs, respectively. (PMID:26343273)
• This review provides information on the pharmacogenetics of MT-RNR1, preceded by a brief synopsis of the mitochondrial genetic system and associated diseases. (PMID:27654872)
• results demonstrate that 19.2% patients with nonsyndromic deafness were caused by mutations in three common deafness genes (GJB2, SLC26A4 and 12S rRNA) in our northern China patient group (PMID:28583500)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.