rs758454871
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PP3_Moderate
The ENST00000268124.11(POLG):c.487C>T(p.Pro163Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000128 in 1,561,606 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 Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P163L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000268124.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLG | NM_002693.3 | c.487C>T | p.Pro163Ser | missense_variant | 2/23 | ENST00000268124.11 | NP_002684.1 | |
POLGARF | NM_001406557.1 | c.542C>T | p.Ala181Val | missense_variant | 2/23 | NP_001393486.1 | ||
POLG | NM_001126131.2 | c.487C>T | p.Pro163Ser | missense_variant | 2/23 | NP_001119603.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POLG | ENST00000268124.11 | c.487C>T | p.Pro163Ser | missense_variant | 2/23 | 1 | NM_002693.3 | ENSP00000268124 | P1 | |
POLGARF | ENST00000706918.1 | c.542C>T | p.Ala181Val | missense_variant | 1/2 | ENSP00000516626 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000291 AC: 5AN: 171530Hom.: 0 AF XY: 0.0000425 AC XY: 4AN XY: 94192
GnomAD4 exome AF: 0.0000106 AC: 15AN: 1409366Hom.: 0 Cov.: 31 AF XY: 0.0000129 AC XY: 9AN XY: 696018
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152240Hom.: 0 Cov.: 34 AF XY: 0.0000538 AC XY: 4AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 27, 2023 | Variant summary: POLG c.487C>T (p.Pro163Ser) results in a non-conservative amino acid change located in the DNA mitochondrial polymerase, exonuclease domain (IPR041336) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.9e-05 in 171530 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.487C>T has been reported in the literature in an individual affected with POLG Related condition (example: Woodbridge_2013). These data do not allow any conclusion about variant significance. One publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (example: Kasahara_2017). The following publications have been ascertained in the context of this evaluation (PMID: 27987238, 22647225). Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 28, 2018 | - - |
Progressive sclerosing poliodystrophy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 17, 2023 | Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt POLG protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 586365). This missense change has been observed in individual(s) with chronic progressiveexternal ophthalmoplegia, seizure, neuropathy, and ataxia (PMID: 22647225). This variant is present in population databases (rs758454871, gnomAD 0.01%). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 163 of the POLG protein (p.Pro163Ser). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at