chrM-9261-A-G

Position:

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The ENST00000362079.2(MT-CO3):ā€‹c.55A>Gā€‹(p.Thr19Ala) variant causes a missense 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 Uncertain significance (ā˜…).

Frequency

Mitomap GenBank:
š‘“ 0.0 ( AC: 3 )

Consequence

MT-CO3
ENST00000362079.2 missense

Scores

Apogee2
Benign
0.051

Clinical Significance

Uncertain significance criteria provided, single submitter U:1
No linked disesase in Mitomap

Conservation

PhyloP100: 3.41
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very low frequency in mitomap database: 0.0
BP4
Apogee2 supports a benign effect, 0.050948717 < 0.5 .

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COX3COX3.1 use as main transcriptc.55A>G p.Thr19Ala missense_variant 1/1 YP_003024032.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MT-CO3ENST00000362079.2 linkuse as main transcriptc.55A>G p.Thr19Ala missense_variant 1/1 ENSP00000354982 P1

Frequencies

GnomAD4 exome
Cov.:
0
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.
Mitomap GenBank
AF:
0.0
AC:
3
Gnomad homoplasmic
AF:
0.0
AC:
0
AN:
56429
Gnomad heteroplasmic
AF:
0.000018
AC:
1
AN:
56429

Mitomap

No disease associated.

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Leigh syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWong Mito Lab, Molecular and Human Genetics, Baylor College of MedicineOct 17, 2019The NC_012920.1:m.9261A>G (YP_003024032.1:p.Thr19Ala) variant in MTCO3 gene is interpretated to be a Uncertain Significance variant based on the modified ACMG guidelines (unpublished). This variant meets the following evidence codes: BP4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Apogee2
Benign
0.051
Hmtvar
Benign
0.12
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
-0.31
T
DEOGEN2
Benign
0.067
T
LIST_S2
Benign
0.60
T
MutationAssessor
Uncertain
2.5
M
MutationTaster
Benign
1.0
N
PROVEAN
Uncertain
-3.1
D
Sift
Pathogenic
0.0
D
Sift4G
Uncertain
0.029
D
GERP RS
3.6
Varity_R
0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1603222202; hg19: chrM-9262; API