chrM-7587-T-C
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP3PP5
The ENST00000361739.1(MT-CO2):c.2T>C(p.Met1?) variant causes a start lost change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Mitomap GenBank:
Absent
Consequence
MT-CO2
ENST00000361739.1 start_lost
ENST00000361739.1 start_lost
Scores
Apogee2
Pathogenic
Clinical Significance
Mitochondrial-Encephalomyopathy
Conservation
PhyloP100: 7.73
Genes affected
MT-CO2 (HGNC:7421): (mitochondrially encoded cytochrome c oxidase II) Contributes to cytochrome-c oxidase activity. Predicted to be involved in mitochondrial electron transport, cytochrome c to oxygen and positive regulation of vasoconstriction. Located in mitochondrial inner membrane. Part of respiratory chain complex IV. Biomarker of Huntington's disease and stomach cancer. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Start lost variant, no new inframe start found.
PM2
?
No frequency data in Mitomap. Probably very rare.
PP3
?
Apogee2 supports a deletorius effect, 0.8750365 >= 0.5 .
PP5
?
Variant M-7587-T-C is Pathogenic according to our data. Variant chrM-7587-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 9658.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COX2 | COX2.1 use as main transcript | c.2T>C | p.Met1? | start_lost | 1/1 | ||
TRND | TRND.1 use as main transcript | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CO2 | ENST00000361739.1 | c.2T>C | p.Met1? | start_lost | 1/1 | P1 | |||
MT-TD | ENST00000387419.1 | downstream_gene_variant |
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
Mitochondrial-Encephalomyopathy
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Mitochondrial complex IV deficiency, nuclear type 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 1999 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Pathogenic
Hmtvar
Pathogenic
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Uncertain
D
MutationTaster
Benign
A
PROVEAN
Pathogenic
D
Sift
Pathogenic
D
Sift4G
Pathogenic
D
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at