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 carbohydrate utilization; and regulation of phosphate metabolic process. Located in extracellular space; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

GeneReviews OMIM ResearchGenerating clinical summary…

DNmechanism

Clinical Summary— MT-RNR1

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Gene-Disease Validity (ClinGen)

mitochondrial disease · MTDefinitive

Definitive — sufficient evidence for diagnostic panels

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ClinVar Variants

2 unique Pathogenic / Likely Pathogenic· 14 VUS of 81 total submissions

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Clinical Trials

3 active or recruiting trials — potential therapeutic options may be available

Explore recent and relevant literature in Research Assistant →

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GeneReview available — MT-RNR1

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

This gene — mechanism propensity

0.6648th %ile

GOF

0.5366th %ile

LOF

0.2969th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

81 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic2

VUS14

Likely Benign39

Benign24

Pathogenic

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	—	—	—	—	2
Likely Pathogenic	—	—	—	—	0
VUS	—	—	—	—	14
Likely Benign	—	—	—	—	39
Benign	—	—	—	—	24
Total	—				79

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

1 pathogenic / likely-pathogenic (of 2) ClinVar copy-number / structural variants overlap MT-RNR1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →

Protein Context — Lollipop Plot

MT-RNR1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

MITOMAP Disease Variants — MT-RNR1

MITOMAP ↗

Variant	AA	Disease	Status	GenBank
m.653G>-	—	Atherosclerosis risk	Reported	0.000%
m.653G>GG	—	Atherosclerosis study	Reported	0.000%
m.663A>G	—	Coronary atherosclerosis risk	Reported	279.690%
m.669T>C	—	DEAF	Reported	18.530%
m.721T>C	—	Possibly LVNC-associated	Reported	22.060%
m.735A>G	—	DEAF	Reported	11.790%
m.745A>G	—	DEAF-associated	Reported	5.970%
m.747A>G	—	DEAF-associated	Reported	1.680%
m.750A>A	—	SZ-associated	Reported	143.370%
m.773T>C	—	Possible association with sepsis	Reported	0.920%
m.792C>T	—	Increased risk of nonsyndromic deafness	Reported	0.770%
m.801A>G	—	DEAF-associated	Reported	1.230%
m.827A>G	—	DEAF	Conflicting reports	257.180%
m.839A>G	—	DEAF-associated	Reported	1.070%
m.850T>C	—	Possibly LVNC-associated	Reported	18.990%
m.856A>G	—	LHON helper / AD / DEAF-associated	Reported	2.760%
m.869C>T	—	found in 1 HCM patient	Reported	14.250%
m.921T>C	—	Possibly LVNC-associated	Reported	71.230%
m.955A>C	—	Possible association with sepsis	Reported	0.310%
m.960C>CC	—	Possibly DEAF-associated	Reported	62.030%
m.960C>-	—	Possibly DEAF-associated	Reported	9.190%
m.961T>G	—	Possibly DEAF-associated	Unclear	36.000%
m.961T>C	—	DEAF, possibly LVNC-associated	Unclear	87.920%
m.961T>CC	—	DEAF / AD-associated / intellectual disability	Reported [LB]	0.000%
m.965C>CC	—	DEAF	Unclear	0.150%
m.988G>A	—	Possible DEAF risk factor	Reported	8.880%
m.990T>C	—	DEAF	Reported	7.200%
m.1005T>C	—	DEAF	Unclear	44.270%
m.1019A>G	—	Ancillary variant in mild optic neuropathy	Reported	3.370%
m.1027A>G	—	DEAF-associated	Reported [VUS]	3.520%
m.1095T>C	—	SNHL	Unclear	10.420%
m.1116A>G	—	DEAF	Reported	1.530%
m.1119T>C	—	Possible role in high altitude sickness	Reported	51.770%
m.1180T>G	—	Possibly DEAF-associated	Reported	0.000%
m.1183T>C	—	Ancillary variant in mild optic neuropathy	Reported	0.610%
m.1192C>A	—	DEAF-associated	Reported	2.300%
m.1192C>T	—	DEAF-associated	Reported	2.300%
m.1226C>G	—	Possibly DEAF-associated	Reported	0.000%
m.1227G>A	—	Translation disruption in cancer cells	Reported	0.000%
m.1291T>C	—	DEAF	Unclear	8.580%
m.1310C>T	—	DEAF-associated	Reported	5.970%
m.1331A>G	—	DEAF-associated	Reported	3.060%
m.1349T>G	—	DEAF	Reported	0.000%
m.1374A>G	—	DEAF-associated	Reported	0.150%
m.1382A>C	—	Longevity / T2D susceptibility	Reported	30.940%
m.1391T>C	—	found in 1 HCM patient	Reported	21.440%
m.1413T>C	—	DEAF-associated	Reported	14.090%
m.1420T>G	—	DEAF	Reported	0.000%
m.1438A>A	—	SZ-associated	Reported	445.730%
m.1452T>C	—	DEAF-associated	Reported	8.420%
m.1453A>G	—	Possible DEAF risk factor	Reported	17.460%
m.1492A>C	—	DEAF	Reported	0.000%
m.1494C>T	—	DEAF	Cfrm [LP]	0.770%
m.1517A>C	—	DEAF	Reported	0.000%
m.1537C>T	—	DEAF; intellectual disability	Reported	1.380%
m.1544A>T	—	DEAF	Reported	0.000%
m.1546A>T	—	DEAF	Reported	0.000%
m.1554G>A	—	DEAF	Reported	0.000%
m.1555A>G	—	DEAF; autism spectrum intellectual disability; possibly antiatherosclerotic	Cfrm [P]	13.330%
m.1556C>T	—	found in 1 HCM patient	Reported	1.990%
m.1575T>G	—	DEAF	Reported	0.000%
m.1577T>G	—	DEAF	Reported	0.000%