MRM3

mitochondrial rRNA methyltransferase 3, the group of SPOUT methyltransferase domain containing

Basic information

Region (hg38): 17:782353-792509

Previous symbols: [ "RNMTL1" ]

Links

ENSG00000171861 ∙ NCBI:55178 ∙ OMIM:612600 ∙ HGNC:18485 ∙ Uniprot:Q9HC36 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRM3 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in MRM3

This is a list of pathogenic ClinVar variants found in the MRM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-782535-G-C		not specified	Uncertain significance (Sep 27, 2021)
17-791665-G-T		not specified	Uncertain significance (Jun 21, 2021)
17-791855-C-T		not specified	Uncertain significance (Jul 06, 2021)
17-791956-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRM3	protein_coding	protein_coding	ENST00000304478	4	10237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.54e-10	0.123	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.273	266	254	1.05	0.0000140	2728
Missense in Polyphen		101	102.07	0.98953		1061
Synonymous	-0.648	118	109	1.08	0.00000654	868
Loss of Function	0.301	15	16.3	0.919	8.03e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000540	0.000539
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000326	0.000326
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000335	0.000334
Middle Eastern	0.000326	0.000326
South Asian	0.0000980	0.0000980
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent 2'-O-ribose methyltransferase that catalyzes the formation of 2'-O- methylguanosine at position 1370 (Gm1370) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl transferase domain of the mtLSU rRNA. {ECO:0000269|PubMed:24036117, ECO:0000269|PubMed:25009282, ECO:0000269|PubMed:25074936}.
• Pathway: rRNA processing;rRNA modification in the mitochondrion;Metabolism of RNA;rRNA processing in the mitochondrion (Consensus)

Intolerance Scores

• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.36

Haploinsufficiency Scores

• pHI: 0.0876
• hipred: N
• hipred_score: 0.144
• ghis: 0.464

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Mrm3
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype

Gene ontology

• Biological process: rRNA 2'-O-methylation
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: RNA binding;protein binding;rRNA (guanosine-2'-O-)-methyltransferase activity