MT-RNR1

Chr MT

s-rRNA

Also known as: MTRNR1

NCBI Gene: 4549 ENSG00000211459 UniProt: A0A0C5B5G6 OMIM: 561000

This gene encodes the mitochondrial 12S ribosomal RNA, which forms part of the small mitoribosomal subunit and is essential for translation of all mitochondrial DNA-encoded proteins. Mutations cause non-syndromic sensorineural hearing loss and aminoglycoside-induced ototoxicity, with the m.1555A>G variant being particularly clinically significant as aminoglycoside exposure leads to irreversible hearing loss in carriers. Inheritance is maternal through the mitochondrial genome.

GeneReviews OMIM ResearchSummary from Curated mito context

Enables DNA binding activity and DNA-binding transcription factor binding activity. Involved in several processes, including osteoblast proliferation; regulation of phosphorus metabolic process; and skeletal muscle tissue growth. Located in mitochondrion; nucleus; and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

GeneReviews OMIM ResearchGenerating clinical summary…

Clinical highlights

Management implications

Carriers of the three CPIC increased-risk variants can lose hearing permanently after standard aminoglycoside doses, even a single dose.Avoid aminoglycosides unless the infection's severity outweighs the risk of permanent hearing loss and there is no safe or effective alternative (CPIC, strong). Any heteroplasmy level counts. Other MT-RNR1 variants are uncertain- or normal-risk.

MT-RNR1: aminoglycoside antibiotics contraindicated

Gene–disease validity (ClinGen)

Definitive · mitochondrial disease · MT · ClinGen 2024

Active trials

Pubs (1 yr)

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P/LP submissions

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P/LP missense

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LOEUF

Mechanism· predicted

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GeneReview available — MT-RNR1

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Treatment implicationsContraindication

Aminoglycoside-induced hearing loss (MT-RNR1 m.1555A>G, m.1494C>T, m.1095T>C)

Avoid aminoglycosides unless the infection's severity outweighs the risk of permanent hearing loss and there is no safe or effective alternative (CPIC, strong). Any heteroplasmy level counts. Other MT-RNR1 variants are uncertain- or normal-risk.

Carriers of the three CPIC increased-risk variants can lose hearing permanently after standard aminoglycoside doses, even a single dose.

Avoid

aminoglycoside antibiotics (gentamicin, tobramycin, amikacin and others) in carriers of an increased-risk variant

McDermott et al. 2022, CPIC guideline, Clin Pharmacol Ther (PMID 34032273). Confirm with a neurologist and current guidelines. Functional class (GOF/LOF) is from published functional/segregation data, never inferred from the variant. As of 2026-10. Curated from the clinical genetics/neurology literature (cited per gene). Decision-support, not prescribing.

Nuclear-gene analyses omitted

MT-RNR1 is a mitochondrial rRNA gene. gnomAD constraint, carrier burden and exome coverage, the ClinVar type breakdown, the protein lollipop, AlphaFold and transcript-architecture views are built for nuclear genes and are not shown. Population data for mtDNA variants (gnomAD v3.1, homoplasmy and heteroplasmy) is on each variant page.

Where it sits in the mitochondrial genome

Tap or hover a gene, landmark or tick; genes open their page, ticks their variant.

proteinrRNAtRNAouter ring H-strand · inner L-strandMITOMAP confirmedreported (as of 2026-10-07)

37 genes from Ensembl (rCRS numbering, matched to MITOMAP’s Gene Loci); landmarks and disease alleles from MITOMAP (CC BY 3.0). Circular layout after MitoWheel.

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

MITOMAP Disease Variants — MT-RNR1

Live table ↗

Variant	Disease	Status	GenBank seqs
m.653G>GG	Atherosclerosis study	Reported	0
m.653G>-	Atherosclerosis risk	Reported	0
m.663A>G	Coronary atherosclerosis risk	Reported	1,842
m.669T>C	DEAF	Reported	125
m.721T>C	Possibly LVNC-associated	Reported	158
m.735A>G	DEAF	Reported	79
m.745A>G	DEAF-associated	Reported	40
m.747A>G	DEAF-associated	Reported	11
m.750A>A	SZ-associated	Reported	970
m.773T>C	Possible association with sepsis	Reported	7
m.792C>T	Increased risk of nonsyndromic deafness	Reported	6
m.801A>G	DEAF-associated	Reported	8
m.827A>G	DEAF	Conflicting reports	1,730
m.839A>G	DEAF-associated	Reported	9
m.850T>C	Possibly LVNC-associated	Reported	131
m.856A>G	LHON helper / AD / DEAF-associated	Reported	18
m.869C>T	found in 1 HCM patient	Reported	95
m.921T>C	Possibly LVNC-associated	Reported	515
m.955A>C	Possible association with sepsis	Reported	2
m.960C>-	Possibly DEAF-associated	Reported	66
m.960C>CC	Possibly DEAF-associated	Reported	409
m.961T>C	DEAF, possibly LVNC-associated	Unclear	617
m.961T>CC	DEAF / AD-associated / intellectual disability	Likely benign · reported	0
m.961T>G	Possibly DEAF-associated	Unclear	236
m.965C>CC	DEAF	Unclear	1
m.988G>A	Possible DEAF risk factor	Reported	58
m.990T>C	DEAF	Reported	49
m.1005T>C	DEAF	Unclear	289
m.1019A>G	Ancillary variant in mild optic neuropathy	Reported	22
m.1027A>G	DEAF-associated	Uncertain significance · reported	23
m.1095T>C	SNHL	Unclear	74
m.1116A>G	DEAF	Reported	10
m.1119T>C	Possible role in high altitude sickness	Reported	341
m.1180T>G	Possibly DEAF-associated	Reported	0
m.1183T>C	Ancillary variant in mild optic neuropathy	Reported	4
m.1192C>T	DEAF-associated	Reported	20
m.1192C>A	DEAF-associated	Reported	15
m.1226C>G	Possibly DEAF-associated	Reported	0
m.1227G>A	Translation disruption in cancer cells	Reported	0
m.1291T>C	DEAF	Unclear	61
m.1310C>T	DEAF-associated	Reported	40
m.1331A>G	DEAF-associated	Reported	20
m.1349T>G	DEAF	Reported	0
m.1374A>G	DEAF-associated	Reported	1
m.1382A>C	Longevity / T2D susceptibility	Reported	202
m.1391T>C	found in 1 HCM patient	Reported	140
m.1413T>C	DEAF-associated	Reported	127
m.1420T>G	DEAF	Reported	0
m.1438A>A	SZ-associated	Reported	3,056
m.1452T>C	DEAF-associated	Reported	55
m.1453A>G	Possible DEAF risk factor	Reported	114
m.1492A>C	DEAF	Reported	0
m.1494C>T	DEAF	Likely pathogenic · confirmed	5
m.1517A>C	DEAF	Reported	0
m.1537C>T	DEAF; intellectual disability	Reported	10
m.1544A>T	DEAF	Reported	0
m.1546A>T	DEAF	Reported	0
m.1554G>A	DEAF	Reported	0
m.1555A>G	DEAF; autism spectrum intellectual disability; possibly antiatherosclerotic	Pathogenic · confirmed	92
m.1556C>T	found in 1 HCM patient	Reported	14
m.1575T>G	DEAF	Reported	0
m.1577T>G	DEAF	Reported	0