Variant M-7680-T-TGTC details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000361739.1(MT-CO2):c.95_96insGTC(p.Phe32delinsLeuSer) variant causes a protein altering change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Mitomap GenBank:

Absent

Consequence

MT-CO2
ENST00000361739.1 protein_altering

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:1

No linked disesase in Mitomap

Conservation

PhyloP100: -2.56

Variant links:

Genes affected

COX2 (HGNC:):

COX2 links:

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]

MT-CO2 links:

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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-7680-T-TGTC is Pathogenic according to our data. Variant chrM-7680-T-TGTC is described in ClinVar as [Pathogenic]. Clinvar id is 590997.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.95_96insGTC	p.Phe32delinsLeuSer	protein_altering_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-CO2	ENST00000361739.1 linkuse as main transcript	c.95_96insGTC	p.Phe32delinsLeuSer	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

Abnormal mitral valve physiology

Pathogenic:1

Pathogenic, no assertion criteria provided

case-control

Molecular Biology Laboratory, University of Basrah

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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.