M-9247-G-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The ENST00000362079.2(MT-CO3):c.41G>C(p.Ser14Thr) variant causes a missense change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S14N) has been classified as Uncertain significance.
Frequency
Mitomap GenBank:
Absent
Consequence
MT-CO3
ENST00000362079.2 missense
ENST00000362079.2 missense
Scores
Apogee2
Uncertain
Clinical Significance
No linked disesase in Mitomap
Conservation
PhyloP100: 7.72
Genes affected
MT-CO3 (HGNC:7422): (mitochondrially encoded cytochrome c oxidase III) Predicted to enable electron transfer activity and oxidoreduction-driven active transmembrane transporter activity. Involved in respiratory chain complex IV assembly. Part of respiratory chain complex IV. Implicated in MELAS syndrome. [provided by Alliance of Genome Resources, Apr 2022]
MT-ATP6 (HGNC:7414): (mitochondrially encoded ATP synthase 6) Contributes to proton-transporting ATP synthase activity, rotational mechanism. Involved in mitochondrial ATP synthesis coupled proton transport. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in Leber hereditary optic neuropathy; NARP syndrome; Parkinson's disease; multiple sclerosis; and systemic lupus erythematosus. [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
No frequency data in Mitomap. Probably very rare.
PP3
Apogee2 supports a deletorius effect, 0.50182635 >= 0.5 .
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COX3 | COX3.1 use as main transcript | c.41G>C | p.Ser14Thr | missense_variant | 1/1 | YP_003024032.1 | ||
ATP6 | ATP6.1 use as main transcript | downstream_gene_variant | YP_003024031.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MT-CO3 | ENST00000362079.2 | c.41G>C | p.Ser14Thr | missense_variant | 1/1 | ENSP00000354982 | P1 | |||
MT-ATP6 | ENST00000361899.2 | downstream_gene_variant | ENSP00000354632 | 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
No disease associated.
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Juvenile myopathy, encephalopathy, lactic acidosis AND stroke Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | MGZ Medical Genetics Center | Dec 01, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Apogee2
Uncertain
Hmtvar
Pathogenic
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
DEOGEN2
Benign
T
LIST_S2
Benign
T
MutationAssessor
Pathogenic
H
MutationTaster
Benign
N
PROVEAN
Uncertain
D
Sift
Pathogenic
D
Sift4G
Pathogenic
D
GERP RS
Varity_R
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.