M-12264-C-T
Variant names:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PP5_Very_Strong
Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 0 )
Consequence
TRNS2
splice_region, synonymous
splice_region, synonymous
Scores
Mitotip
Pathogenic
Clinical Significance
Multisystem-Disease-with-Cataracts-/-Myopathy+epilepsy+DEAF+atypical-autism
Conservation
PhyloP100: -0.0400
Genes affected
TRNS2 (HGNC:7498): (mitochondrially encoded tRNA serine 2 (AGU/C))
ND5 (HGNC:7461): (mitochondrially encoded NADH dehydrogenase 5) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Leigh disease; and MELAS syndrome. [provided by Alliance of Genome Resources, Apr 2022]
TRNL2 (HGNC:7491): (mitochondrially encoded tRNA leucine 2 (CUN))
ND4 (HGNC:7459): (mitochondrially encoded NADH dehydrogenase 4) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone and mitochondrial respiratory chain complex I assembly. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Parkinson's disease; macular degeneration; and schizophrenia. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PM2
Very low frequency in mitomap database: 0.0
PP5
Variant M-12264-C-T is Pathogenic according to our data. Variant chrM-12264-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 690178.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNS2 | unassigned_transcript_4813 | c.58C>T | p.???20??? | splice_region_variant, synonymous_variant | Exon 1 of 1 | |||
ND5 | unassigned_transcript_4815 | c.-73C>T | upstream_gene_variant | |||||
TRNL2 | unassigned_transcript_4814 | c.-2C>T | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|
Frequencies
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
AC:
0
Mitomap
Multisystem-Disease-with-Cataracts-/-Myopathy+epilepsy+DEAF+atypical-autism
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
MELAS syndrome Pathogenic:2
May 04, 2022
Mendelics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Jul 12, 2019
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing
The NC_012920.1:m.12264C>T variant in MT-TS2 gene is interpreted to be a Likely Pathogenic variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes reported in the guidelines: PM7, PM9, PM10 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Pathogenic
Hmtvar
Pathogenic
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at