MT-RNR1

mitochondrially encoded 12S rRNA, the group of Mitochondrially encoded ribosomal RNAs

Basic information

Region (hg38): M:648-1601

Previous symbols: [ "MTRNR1" ]

Links

ENSG00000211459 ∙ NCBI:4549 ∙ OMIM:561000 ∙ HGNC:7470 ∙ Uniprot:A0A0C5B5G6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial disease (Definitive), mode of inheritance: Mitochondrial

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, mitochondrial	Maternal	Audiologic/Otolaryngologic; Pharmacogenomic	Mitochondrial variants may involve a variety of sequelae, including hearing impairment, with highly variable age of onset, and for individuals with early-onset hearing impairment, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Aminoglycosides should be avoided	Audiologic/Otolaryngologic; Biochemical; Cardiovascular	7689389; 9039999; 9887373; 9490575; 10326749; 10577941; 9915970; 10521300; 10788333; 11079536; 11313749; 12372057; 12920080; 12624722; 15286157; 14755216; 14681830; 15555598; 15637703; 15708009; 16380089; 16458854; 16631122; 16375862; 16782057; 17341440; 18261986; 18983818
In some individuals, aminoglycoside administration can result in deafness; Individuals have also been reported with cardiomyopathy

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MT-RNR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MT-RNR1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

Variants in MT-RNR1

This is a list of pathogenic ClinVar variants found in the MT-RNR1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
M-663-A-G			Benign (Dec 12, 2018)
M-721-T-C			Likely benign (Aug 17, 2020)
M-750-A-G		Venous thromboembolism	association not found (-)
M-813-A-G			Benign (Feb 18, 2019)
M-827-A-G		Mitochondrial non-syndromic sensorineural hearing loss • Aminoglycoside-induced deafness • Gentamicin response	drug response (Aug 01, 2018)
M-869-C-T			Likely benign (May 10, 2016)
M-930-G-A			Benign (Nov 27, 2018)
M-951-G-A		not specified	Likely benign (Aug 28, 2013)
M-953-T-C		not specified	Likely benign (Mar 02, 2017)
M-954-C-T		not specified	Benign (Nov 27, 2017)
M-955-AC-A		not specified	Likely benign (Sep 01, 2015)
M-955-A-AC		not specified	Likely benign (Nov 17, 2016)
M-956-C-T		not specified	Uncertain significance (Jan 08, 2013)
M-955-A-ACCC		not specified	Likely benign (Apr 18, 2018)
M-959-CCT-C		not specified	Likely benign (Apr 18, 2016)
M-961-T-C		not specified	Benign (Dec 12, 2011)
M-961-T-G		Mitochondrial non-syndromic sensorineural hearing loss • not specified	Likely benign (Feb 06, 2015)
M-962-C-T		not specified	Uncertain significance (Jun 09, 2016)
M-979-C-T		not specified	Likely benign (Jan 14, 2015)
M-980-T-C		not specified	Likely benign (Jan 09, 2018)
M-990-T-C		not specified	Likely benign (Dec 13, 2013)
M-1005-T-C		not specified	Benign (Jun 11, 2013)
M-1007-G-A		not specified	Benign (Sep 05, 2013)
M-1008-A-G		not specified	Likely benign (May 15, 2013)
M-1018-G-A		not specified	Benign (May 29, 2018)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates insulin sensitivity and metabolic homeostasis. Inhibits the folate cycle, thereby reducing de novo purine biosynthesis which leads to the accumulation of the de novo purine synthesis intermediate 5-aminoimidazole-4-carboxamide (AICAR) and the activation of the metabolic regulator 5'-AMP-activated protein kinase (AMPK). Protects against age-dependent and diet-induced insulin resistance as well as diet-induced obesity. {ECO:0000269|PubMed:25738459}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);Ribosome - Homo sapiens (human) (Consensus)

Mouse Genome Informatics

• Gene name: mt-Rnr1

Gene ontology

• Biological process: activation of protein kinase activity;regulation of carbohydrate utilization;purine-containing compound biosynthetic process
• Cellular component: extracellular space