Variant M-9311-T-TGCA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4_SupportingPP5

The ENST00000362079.2(MT-CO3):c.105_106insGCA(p.Phe35_His36insAla) variant causes a inframe insertion change. Variant has been reported in ClinVar as Likely pathogenic (no stars).

Frequency

Mitomap GenBank:

Absent

Consequence

MT-CO3
ENST00000362079.2 inframe_insertion

Scores

Clinical Significance

Likely pathogenic no assertion criteria provided P:1

No linked disesase in Mitomap

Conservation

PhyloP100: 4.80

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2

No frequency data in Mitomap. Probably very rare.

PM4

Nonframeshift variant in NON repetitive region in ENST00000362079.2. Strenght limited to Supporting due to length of the change: 1aa.

PP5

Variant M-9311-T-TGCA is Pathogenic according to our data. Variant chrM-9311-T-TGCA is described in ClinVar as [Likely_pathogenic]. Clinvar id is 590894.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.105_106insGCA	p.Phe35_His36insAla	inframe_insertion	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MT-CO3	ENST00000362079.2 linkuse as main transcript	c.105_106insGCA	p.Phe35_His36insAla	inframe_insertion	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: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Abnormal aortic valve physiology

Pathogenic:1

Likely 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.