chrM-10438-A-G
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The ENST00000387439.1(MT-TR):n.34A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 0 )
Consequence
MT-TR
ENST00000387439.1 non_coding_transcript_exon
ENST00000387439.1 non_coding_transcript_exon
Scores
Mitotip
Uncertain
Clinical Significance
Progressive-Encephalopathy,Non-dystrophic-myopathy
Conservation
PhyloP100: 1.33
Genes affected
MT-TR (HGNC:7496): (mitochondrially encoded tRNA arginine)
MT-ND4L (HGNC:7460): (mitochondrially encoded NADH 4L dehydrogenase) Predicted to enable NADH dehydrogenase (ubiquinone) activity. Predicted to be located in mitochondrial inner membrane. Implicated in Leber hereditary optic neuropathy and diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]
MT-ND3 (HGNC:7458): (mitochondrially encoded NADH dehydrogenase 3) Enables NADH dehydrogenase (ubiquinone) activity. Involved in mitochondrial electron transport, NADH to ubiquinone. Part of mitochondrial respiratory chain complex I. Implicated in Leber hereditary optic neuropathy; Leigh disease; and Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very low frequency in mitomap database: 0.0
PP5
Variant M-10438-A-G is Pathogenic according to our data. Variant chrM-10438-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 9623.Status of the report is criteria_provided_single_submitter, 1 stars.
BP4
Mitotip and hmtvar scores support benign criterium.. Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNR | TRNR.1 use as main transcript | n.34A>G | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MT-TR | ENST00000387439.1 | n.34A>G | non_coding_transcript_exon_variant | 1/1 | ||||||
MT-ND4L | ENST00000361335.1 | upstream_gene_variant | ENSP00000354728 | P1 | ||||||
MT-ND3 | ENST00000361227.2 | downstream_gene_variant | ENSP00000355206 | P1 |
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
Gnomad homoplasmic
AF:
AC:
0
AN:
56432
Gnomad heteroplasmic
AF:
AC:
1
AN:
56432
Mitomap
Progressive-Encephalopathy,Non-dystrophic-myopathy
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Mitochondrial disease Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Mitochondrial encephalomyopathy Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 01, 2004 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Uncertain
Hmtvar
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at