M-9311-T-TGCA

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
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 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 Protein UniProt
COX3COX3.1 use as main transcriptc.105_106insGCA p.Phe35_His36insAla inframe_insertion 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.105_106insGCA p.Phe35_His36insAla inframe_insertion 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

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 providedcase-controlMolecular 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.

Other links and lift over

dbSNP: rs1569484292; hg19: chrM-9312; API