MRM2

mitochondrial rRNA methyltransferase 2, the group of 7BS 2'O-ribose DNA/RNA methyltransferases

Basic information

Region (hg38): 7:2234194-2242205

Previous symbols: [ "FTSJ2" ]

Links

ENSG00000122687 ∙ NCBI:29960 ∙ OMIM:606906 ∙ HGNC:16352 ∙ Uniprot:Q9UI43 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial DNA depletion syndrome 17 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial DAN depletion syndrome 17	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Neurologic	28973171

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MRM2 gene.

• not provided (8 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MRM2 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				3	1	4
missense			5		1	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	3	2

Variants in MRM2

This is a list of pathogenic ClinVar variants found in the MRM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-2235148-C-T		MRM2-related disorder	Benign (Mar 30, 2020)
7-2235236-T-C			Likely benign (Mar 01, 2022)
7-2235297-C-T		not specified	Uncertain significance (Sep 01, 2021)
7-2235298-C-T		Mitochondrial DNA depletion syndrome 17	Pathogenic (Sep 03, 2019)
7-2235376-G-A		not specified	Uncertain significance (Jul 06, 2021)
7-2235542-G-A		MRM2-related disorder	Benign (Dec 23, 2019)
7-2239474-G-A		Mitochondrial DNA depletion syndrome 17	Uncertain significance (Sep 30, 2022)
7-2239579-G-C			Uncertain significance (Mar 21, 2023)
7-2239587-A-G			Likely benign (May 01, 2022)
7-2239588-A-G			Uncertain significance (Oct 04, 2022)
7-2239629-G-A		MRM2-related disorder	Likely benign (Oct 01, 2022)
7-2239684-G-A		MRM2-related disorder	Benign (Oct 29, 2019)
7-2242159-C-T		MRM2-related disorder	Likely benign (Jul 14, 2020)
7-2242161-C-A		Mitochondrial DNA depletion syndrome 17	Pathogenic (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MRM2	protein_coding	protein_coding	ENST00000242257	3	7975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000236	0.536	125705	0	41	125746	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0869	150	153	0.980	0.00000954	1583
Missense in Polyphen		52	56.593	0.91884		608
Synonymous	-0.375	67	63.2	1.06	0.00000410	523
Loss of Function	0.459	6	7.34	0.817	4.65e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000708	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000708	0.000707
South Asian	0.000181	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent 2'-O-ribose methyltransferase that catalyzes the formation of 2'-O- methyluridine at position 1369 (Um1369) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a universally conserved modification in the peptidyl transferase domain of the mtLSU rRNA. {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)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.204
• ghis: 0.643

Essentials

• essential_gene_gene_trap: K

Mouse Genome Informatics

• Gene name: Mrm2

Gene ontology

• Biological process: rRNA 2'-O-methylation;rRNA processing;cell population proliferation;rRNA methylation
• Cellular component: nucleolus;mitochondrion;mitochondrial matrix
• Molecular function: rRNA (uridine-2'-O-)-methyltransferase activity