chrM-616-T-G
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 1 )
Consequence
TRNF
missense
missense
Scores
Mitotip
Pathogenic
Clinical Significance
Maternally-inherited-epilepsy-/-mito-tubulointerstitial-kidney-disease-(MITKD)-/-Gitelman-like-syndrome,Maternally-inherited-epilepsy
Conservation
PhyloP100: 3.71
Genes affected
TRNF (HGNC:7481): (mitochondrially encoded tRNA phenylalanine)
RNR1 (HGNC:7470): (mitochondrially encoded 12S RNA) Enables DNA binding activity and DNA-binding transcription factor binding activity. Involved in several processes, including osteoblast proliferation; regulation of carbohydrate utilization; and regulation of phosphate metabolic process. Located in extracellular space; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
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-616-T-G is Pathogenic according to our data. Variant chrM-616-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 9577.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNF | unassigned_transcript_4784 | c.40T>G | p.Cys14Gly | missense_variant | Exon 1 of 1 | |||
RNR1 | unassigned_transcript_4785 | n.-32T>G | 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:
1
Mitomap
Maternally-inherited-epilepsy-/-mito-tubulointerstitial-kidney-disease-(MITKD)-/-Gitelman-like-syndrome,Maternally-inherited-epilepsy
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Epilepsy, mitochondrial Pathogenic:1
Feb 09, 2010
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Mitotip
Pathogenic
Hmtvar
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at