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GeneBe

M-8560-C-CCCA

Variant summary

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

The ENST00000361899.2(MT-ATP6):c.36_38dup(p.Thr13_Ile13insThr) variant causes a inframe insertion change. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Mitomap GenBank:
Absent

Consequence

MT-ATP6
ENST00000361899.2 inframe_insertion

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:1
No linked disesase in Mitomap

Conservation

PhyloP100: 5.86
Variant links:
Genes affected
MT-ATP8 (HGNC:7415): (mitochondrially encoded ATP synthase 8) Contributes to proton-transporting ATP synthase activity, rotational mechanism. Involved in mitochondrial ATP synthesis coupled proton transport. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in multiple sclerosis and urinary bladder cancer. [provided by Alliance of Genome Resources, Apr 2022]
MT-ATP6 (HGNC:7414): (mitochondrially encoded ATP synthase 6) Contributes to proton-transporting ATP synthase activity, rotational mechanism. Involved in mitochondrial ATP synthesis coupled proton transport. Part of mitochondrial proton-transporting ATP synthase complex. Implicated in Leber hereditary optic neuropathy; NARP syndrome; Parkinson's disease; multiple sclerosis; and systemic lupus erythematosus. [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
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
No frequency data in Mitomap. Probably very rare.
PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Nonframeshift variant in NON repetitive region in ENST00000361899.2. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
    PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation
Variant M-8560-C-CCCA is Pathogenic according to our data. Variant chrM-8560-C-CCCA is described in ClinVar as [Pathogenic]. Clinvar id is 590998.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ATP6ATP6.1 use as main transcriptc.36_38dup p.Thr13_Ile13insThr inframe_insertion 1/1
ATP8ATP8.1 use as main transcriptc.197_199dup p.Pro66dup inframe_insertion 1/1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MT-ATP8ENST00000361851.1 linkuse as main transcriptc.197_199dup p.Pro66dup inframe_insertion 1/1 P1
MT-ATP6ENST00000361899.2 linkuse as main transcriptc.36_38dup p.Thr13_Ile13insThr inframe_insertion 1/1 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: 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 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: rs1569484221; hg19: chrM-8561; API