MITOMAP: Mitochondrial DNA Base Substitution Diseases:
rRNA/tRNA Mutations with Crfm Status

Last Edited: Dec 13, 2024

For Mitomap to assign a status of "Cfrm" to a possibly pathogenic variant, we look for confirming reports which address the criteria outlined in Mitchell et al 2006, Yarham et al 2011, Wong 2007, and Gonzalez-Viogue et al 2014. These criteria include the following: (1) independent reports of two or more unrelated families with evidence of similar disease; (2) evolutionary conservation of the nucleotide (for RNA variants) or amino acid (for coding variants); (3) presence of heteroplasmy; (4) correlation of variant with phenotype / segregation of the mutation with the disease within a family; (5) biochemical defects in complexes I, III, or IV in affected or multiple tissues; (6) functional studies showing differential defects segregating with the mutation (cybrid or single fiber studies); (7) histochemical evidence of a mitochondrial disorder; and (8) for fatal or severe phenotypes, the absence or extremely rare occurrence of the variant in large mtDNA sequence databases. For the exact scoring systems of Yarham et al 2011 and Mitchell et al 2006, please see the respective papers above. A new scoring system is under development for these criteria, and will be linked here once published.

When investigating a novel variant or a variant of uncertain significance (VUS) in cases of suspected mitochondrial disease, further studies which address any or all of the above criteria are strongly recommended. We encourage publication of such case reports as they are extremely helpful to the mitochondrial research community.

The GB frequency data in Mitomap is derived from 61124 GenBank sequences with size greater than 15.4kbp and 80432 Control Region sequences with size 0.4-1.6kbp. These sequences have been pre-loaded into Mitomaster and represent almost all haplogroups known to date. We will be updating and refining this set of sequences on a regular basis. As a caveat, please note that GenBank sequences may not be of equal quality (Yao, et al, 2009), that some of these sequences are from individuals with past, current or future disease, and that this portion of our data set has not been hand-curated by Mitomap.

For more details about the current GenBank sequence set, please see GB Frequency Info.

For information about the predictive MitoTIP scoring for tRNA variants, see MitoTIP Info.

Locus	Disease	Allele	RNA	Homo-plasmy	Hetero-Plasmy	Status	References

583,"MT-TF","MELAS / MM & EXIT","G583A","tRNA Phe","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","5"591,"MT-TF","Gitelman-like syndrome","C591T","tRNA Phe","+","-","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","1"616,"MT-TF","Maternally inherited epilepsy / mito tubulointerstitial kidney disease (MITKD) / Gitelman-like syndrome","T616C","tRNA Phe","+","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","6"1494,"MT-RNR1","DEAF","C1494T","12S rRNA","+","-","Cfrm [LP]","N/A","0.008%
(0.000%)","5 (0)","34"1555,"MT-RNR1","DEAF; autism spectrum intellectual disability; possibly antiatherosclerotic","A1555G","12S rRNA","+","+","Cfrm [P]","N/A","0.139%
(0.000%)","85 (0)","161"1606,"MT-TV","AMDF","G1606A","tRNA Val","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","5"1624,"MT-TV","Leigh Syndrome","C1624T","tRNA Val","+","-","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","6"1630,"MT-TV","MNGIE-like disease / MELAS","A1630G","tRNA Val","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","9"1644,"MT-TV","Leigh Syndrome / HCM / MELAS","G1644A","tRNA Val","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","6"3242,"MT-TL1","MM / HCM+renal tubular dysfunction","G3242A","tRNA Leu (UUR)","+","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","13"3243,"MT-TL1","MELAS / Leigh Syndrome / DMDF / MIDD / SNHL / CPEO / MM / FSGS / ASD / Cardiac+multi-organ dysfunction","A3243G","tRNA Leu (UUR)","-","+","Cfrm [P]","Pathogenic ","0.015%
(0.000%)","9 (0)","477"3243,"MT-TL1","MM / MELAS / SNHL / CPEO","A3243T","tRNA Leu (UUR)","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","12"3251,"MT-TL1","MM / MELAS with chorea-ballism","A3251G","tRNA Leu (UUR)","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","7"3252,"MT-TL1","MELAS","A3252G","tRNA Leu (UUR)","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","7"3255,"MT-TL1","MERRF / KSS overlap","G3255A","tRNA Leu (UUR)","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","6"3256,"MT-TL1","MELAS; possible atherosclerosis risk","C3256T","tRNA Leu (UUR)","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","21"3258,"MT-TL1","MELAS / Myopathy","T3258C","tRNA Leu (UUR)","-","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","5"3260,"MT-TL1","MMC / MELAS","A3260G","tRNA Leu (UUR)","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","18"3271,"MT-TL1","MELAS / DM / MERRF-like","T3271C","tRNA Leu (UUR)","-","+","Cfrm [P]","Pathogenic ","0.000%
(0.000%)","0 (0)","40"3273,"MT-TL1","PEM / retinal dystrophy in MELAS","T3273del","tRNA Leu (UUR)","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","2"3280,"MT-TL1","Myopathy","A3280G","tRNA Leu (UUR)","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","6"3291,"MT-TL1","MELAS / Myopathy / Deafness+Cognitive Impairment","T3291C","tRNA Leu (UUR)","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","18"3302,"MT-TL1","MM","A3302G","tRNA Leu (UUR)","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","15"3303,"MT-TL1","MMC","C3303T","tRNA Leu (UUR)","+","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","22"4298,"MT-TI","CPEO / MS","G4298A","tRNA Ile","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","11"4300,"MT-TI","MICM","A4300G","tRNA Ile","+","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","11"4308,"MT-TI","CPEO","G4308A","tRNA Ile","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","3"4332,"MT-TQ","Encephalopathy / MELAS","G4332A","tRNA Gln","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","4"4450,"MT-TM","Myopathy / MELAS / Leigh Syndrome / EXIT","G4450A","tRNA Met","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","5"5521,"MT-TW","Mitochondrial myopathy","G5521A","tRNA Trp","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","8"5537,"MT-TW","Leigh Syndrome","A5537insT","tRNA Trp","-","+","Cfrm [LP]","-","0.000%
(0.000%)","0 (0)","7"5556,"MT-TW","Combined OXPHOS defects","G5556A","tRNA Trp","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","3"5650,"MT-TA","Myopathy","G5650A","tRNA Ala","-","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","10"5690,"MT-TN","CPEO+ptosis+proximal myopathy","A5690G","tRNA Asn","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","3"5703,"MT-TN","CPEO / MM","G5703A","tRNA Asn","-","+","Cfrm [P]","Pathogenic ","0.002%
(0.000%)","1 (0)","12"5728,"MT-TN","Multiorgan failure / myopathy","T5728C","tRNA Asn","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","4"7445,"MT-TS1 precursor","SNHL","A7445G","tRNA Ser (UCN) precursor","+","+","Cfrm [P]","-","0.002%
(0.000%)","1 (0)","45"7453,"MT-TS1","Fatal neonatal lactic acidosis / Neonatal lactic acidosis, exercise intolerance, mild ID","G7453A","tRNA Ser (UCN)","+","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","4"7471,"MT-TS1","PEM / AMDF / Motor neuron disease-like","C7471CC","tRNA Ser (UCN)","+","+","Cfrm [P]","-","0.011%
(0.000%)","7 (0)","34"7497,"MT-TS1","MM / EXIT","G7497A","tRNA Ser (UCN)","+","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","8"7510,"MT-TS1","SNHL","T7510C","tRNA Ser (UCN)","-","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","14"7511,"MT-TS1","SNHL/Deafness","T7511C","tRNA Ser (UCN)","+","+","Cfrm [LP]","Pathogenic ","0.003%
(0.000%)","2 (0)","24"7512,"MT-TS1","PEM / MERME / MELAS","T7512C","tRNA Ser (UCN)","+","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","13"8306,"MT-TK","Severe adult-onset multisymptom myopathy / Myoclonic epilepsy","T8306C","tRNA Lys","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","3"8313,"MT-TK","MNGIE-like / Progressive mito cytopathy","G8313A","tRNA Lys","-","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","9"8340,"MT-TK","Myopathy, Exercise Intolerance, CPEO-like /childhood epilepsy with SNHL & eye disease","G8340A","tRNA Lys","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","12"8344,"MT-TK","MERRF; Other - LD / depressive mood disorder / leukoencephalopathy / HiCM / lipomas","A8344G","tRNA Lys","-","+","Cfrm [P]","Pathogenic ","0.007%
(0.000%)","4 (0)","155"8356,"MT-TK","MERRF","T8356C","tRNA Lys","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","12"8363,"MT-TK","MICM+DEAF / MERRF / Autism / Leigh Syndrome / Ataxia","G8363A","tRNA Lys","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","23"10010,"MT-TG","PEM","T10010C","tRNA Gly","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","11"12147,"MT-TH","MERRF-MELAS / Encephalopathy","G12147A","tRNA His","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","6"12201,"MT-TH","Maternally inherited non-syndromic deafness","T12201C","tRNA His","-","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","10"12258,"MT-TS2","DMDF / RP+SNHL","C12258A","tRNA Ser (AGY)","-","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","9"12276,"MT-TL2","CPEO","G12276A","tRNA Leu (CUN)","-","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","4"12294,"MT-TL2","CPEO / EXIT+Ophthalmoplegia","G12294A","tRNA Leu (CUN)","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","2"12315,"MT-TL2","CPEO / KSS / possible carotid atherosclerosis risk, trend toward myocardial infarction risk","G12315A","tRNA Leu (CUN)","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","15"12316,"MT-TL2","CPEO / mitochondrial myopathy","G12316A","tRNA Leu (CUN)","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","3"14674,"MT-TE","Reversible COX deficiency myopathy","T14674C","tRNA Glu","+","-","Cfrm [LP]","Pathogenic ","0.016%
(0.000%)","10 (0)","16"14709,"MT-TE","MM+DMDF / Encephalomyopathy / Dementia+diabetes+ophthalmoplegia","T14709C","tRNA Glu","+","+","Cfrm [LP]","Pathogenic ","0.002%
(0.000%)","1 (0)","28"14710,"MT-TE","Encephalomyopathy + Retinopathy","G14710A","tRNA Glu","-","+","Cfrm [VUS*]","Pathogenic ","0.000%
(0.000%)","0 (0)","6"15923,"MT-TT","LIMM / MERRF / mito disease","A15923G","tRNA Thr","+","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","5"15990,"MT-TP","MM / PEO","C15990T","tRNA Pro","-","+","Cfrm [LP]","Pathogenic ","0.000%
(0.000%)","0 (0)","5"
♣ ClinGen Pathogenicity Rating ^NEW

As a member of the mtDNA Variant Curation Expert Panel for ClinGen, we are adding the calculated ClinGen pathogenicity ratings after VCEP curation. This will be shown in brackets in the Status column, for example, "Reported [VUS]", "Cfrm [LP]", etc., as the ClinGen scoring becomes available. The ClinGen VCEP may update this scoring from time to time if additional supporting evidence is published. The following abbreviations are used: B, Benign; LB, Likely Benign; VUS, Variant of Uncertain Significance; LP, Likely Pathogenic; P, Pathogenic. The criteria used in the ClinGen curations may be found in McCormick et al, 2020, DOI: 10.1002/humu.24107. Note that the ClinGen scoring gives fewer points than Mitomap does for many types of evidence, e.g., cybrid & other functional studies, in-silico tools, absence in large databases, heteroplasmy, de-novo requirements, and case numbers.

Notes

LHON	Leber Hereditary Optic Neuropathy	MM	Mitochondrial Myopathy
AD	Alzeimer's Disease	LIMM	Lethal Infantile Mitochondrial Myopathy
ADPD	Alzeimer's Disease and Parkinsons's Disease	MMC	Maternal Myopathy and Cardiomyopathy
NARP	Neurogenic muscle weakness, Ataxia, and Retinitis Pigmentosa; alternate phenotype at this locus is reported as Leigh Disease	FICP	Fatal Infantile Cardiomyopathy Plus, a MELAS-associated cardiomyopathy
MELAS	Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like episodes	LDYT	Leber's hereditary optic neuropathy and DYsTonia
MERRF	Myoclonic Epilepsy and Ragged Red Muscle Fibers	MHCM	Maternally inherited Hypertrophic CardioMyopathy
CPEO	Chronic Progressive External Ophthalmoplegia	KSS	Kearns Sayre Syndrome
DM	Diabetes Mellitus	DMDF	Diabetes Mellitus + DeaFness
CIPO	Chronic Intestinal Pseudoobstruction with myopathy and Ophthalmoplegia	DEAF	Maternally inherited DEAFness or aminoglycoside-induced DEAFness
PEM	Progressive encephalopathy	SNHL	SensoriNeural Hearing Loss

• Homoplasmy = pure mutant mtDNAs.
• Heteroplasmy = mixture of mutant and normal mtDNAs.
• nd = not determined.
• "Reported" status indicates that one or more publications have considered the mutation as possibly pathologic. This is not an assignment of pathogenicity by MITOMAP but is a report of literature. Previously, mutations with this status were termed "Prov" (provisional).
• "Cfrm"(confirmed) status indicates that at least two or more independent laboratories have published reports on the pathogenicity of a specific mutation. These mutations are generally accepted by the mitochondrial research community as being pathogenic. A status of "Cfrm" is not an assignment of pathogenicity by MITOMAP but is a report of published literature. Researchers and clinicians are cautioned that additional data and/or analysis may still be necessary to confirm the pathological significance of some of these mutations.
• "P.M." (point mutation/polymorphism) status indicates that some published reports have determined the mutation to be a non-pathogenic polymorphism.