Variant M-9273-T-TATC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

The ENST00000362079.2(MT-CO3):c.67_68insATC(p.Ser23delinsTyrPro) variant causes a protein altering change. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Mitomap GenBank:

Absent

Consequence

MT-CO3
ENST00000362079.2 protein_altering

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:1

No linked disesase in Mitomap

Conservation

PhyloP100: 4.76

Variant links:

Genes affected

COX3 (HGNC:):

COX3 links:

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-CO3 links:

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.

PP5

Variant M-9273-T-TATC is Pathogenic according to our data. Variant chrM-9273-T-TATC is described in ClinVar as [Pathogenic]. Clinvar id is 599028.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COX3	COX3.1 use as main transcript	c.67_68insATC	p.Ser23delinsTyrPro	protein_altering_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-CO3	ENST00000362079.2 linkuse as main transcript	c.67_68insATC	p.Ser23delinsTyrPro	protein_altering_variant	1/1			P1

Frequencies

GnomAD4 exome

Cov.:

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

Mitomap

No disease associated.

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Tetralogy of Fallot

Pathogenic:1

Pathogenic, no assertion criteria provided

case-control

Molecular Biology Laboratory, University of Basrah

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.