rs104894632
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP3_StrongPP5_Moderate
The NM_007215.4(POLG2):c.1352G>A(p.Gly451Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G451R) has been classified as Uncertain significance.
Frequency
Consequence
NM_007215.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLG2 | NM_007215.4 | c.1352G>A | p.Gly451Glu | missense_variant | 8/8 | ENST00000539111.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLG2 | ENST00000539111.7 | c.1352G>A | p.Gly451Glu | missense_variant | 8/8 | 1 | NM_007215.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461692Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727144
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
POLG2-Related Disorders Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 23, 2023 | Variant summary: POLG2 c.1352G>A (p.Gly451Glu) results in a non-conservative amino acid change located in the Anticodon-binding domain (IPR004154) and C-terminal domain (IPR042064) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251208 control chromosomes (gnomAD). c.1352G>A has been reported in the literature in at least one heterozygous individual affected with late-onset autosomal-dominant progressive external ophthalmoplegia with a positive family history of disease (e.g., Longley_2006). These data suggest the variant may be associated with disease. Several publications report experimental evidence evaluating an impact on protein function, finding that the variant displays a severe defect in its ability to physically associate with the catalytic subunit and is thus unable to enhance processivity of the holoenzyme (e.g., Longley_2006, Chan_2009, Young_2011). Experimental studies also found that the variant displayed a dominant negative effect, leading to loss of homodimeric polymerase gamma acitivty and substantial impairment of heterodimeric activity in complex with the wild-type (Young_2015). The following publications have been ascertained in the context of this evaluation (PMID: 19513667, 16685652, 21138766, 21555342, 26123486). No submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic. - |
Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at