rs397507452
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The ENST00000361624.2(MT-CO1):c.1540A>G(p.Ter514GlyextTer?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Mitomap GenBank:
𝑓 0.0 ( AC: 1 )
Consequence
MT-CO1
ENST00000361624.2 stop_lost
ENST00000361624.2 stop_lost
Scores
Clinical Significance
DEAF
Conservation
PhyloP100: -0.146
Genes affected
MT-CO1 (HGNC:7419): (mitochondrially encoded cytochrome c oxidase I) Contributes to cytochrome-c oxidase activity. Predicted to be involved in electron transport coupled proton transport and mitochondrial electron transport, cytochrome c to oxygen. Part of mitochondrial respiratory chain complex III and mitochondrial respiratory chain complex IV. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very low frequency in mitomap database: 0.0
PP5
?
Variant M-7443-A-G is Pathogenic according to our data. Variant chrM-7443-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 40158.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COX1 | COX1.1 use as main transcript | c.1540A>G | p.Ter514GlyextTer? | stop_lost | 1/1 | ||
TRNS1 | TRNS1.1 use as main transcript | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT-CO1 | ENST00000361624.2 | c.1540A>G | p.Ter514GlyextTer? | stop_lost | 1/1 | P1 | |||
MT-TS1 | ENST00000387416.2 | 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 GenBank
AF:
AC:
1
Gnomad homoplasmic
AF:
AC:
1
AN:
56434
Gnomad heteroplasmic
AF:
AC:
0
AN:
56434
Mitomap
DEAF
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Mitochondrial non-syndromic sensorineural hearing loss Pathogenic:1Other:1
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
MutationTaster
Benign
A
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at