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POLG
Final classification
VUS
POLG c.3436C>T · p.Arg1146Cys
POLG

NM_001126131.1:c.3436C>T (p.Arg1146Cys) is a missense variant in exon 21 of POLG, encoding the catalytic subunit of mitochondrial DNA polymerase gamma.

Gene
POLG
Transcript
NM_001126131.1
HGVS · transcript:coding
NM_001126131.1:c.3436C>T
Consequence
N/A
GRCh38
chr15:89318587 G>A
GRCh37
chr15:89861818 G>A
Basis ClinGen Mitochondrial Disease Nuclear and Mitochondrial Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1_ntDNA v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PP3 supporting, BS1 strong; combination = 1 supporting + 1 strong benign, which maps to VUS.
ClinGen Mitochondrial Disease Nuclear and Mitochondrial Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1_ntDNA v1.0.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PP3 supporting, BS1 strong; combination = 1 supporting + 1 strong benign, which maps to VUS.
Classification rationale
PP3 BS1 VUS
POLG c.3436C>T

NM_001126131.1:c.3436C>T (p.Arg1146Cys) is a missense variant in exon 21 of POLG, encoding the catalytic subunit of mitochondrial DNA polymerase gamma. This variant is present in gnomAD v2.1 at an overall allele frequency of 0.01874% (53/282,776 alleles, 0 homozygotes), with the highest subpopulation frequency of 0.03508% in the East Asian population, exceeding the VCEP BS1 threshold of >0.0092%.1 The variant is absent from gnomAD v4.1 and gnomAD-Canada.2 The REVEL in silico prediction score of 0.915 exceeds the VCEP threshold of >0.75 for PP3 at Supporting strength, indicating computational evidence of a deleterious effect.3 SpliceAI predicts no splicing impact (max delta score = 0.00).4 This variant has been reported in ClinVar (VariationID: 21313) as a Variant of Uncertain Significance by 8 clinical laboratories and as Benign by 1 clinical laboratory (review status: criteria provided, single submitter).5 The variant has been observed once in the COSMIC somatic cancer database (COSV51525791). Amino acid position 1146 is not located within any of the POLG functional domains specified by the VCEP (TPP binding site, heterodimer interface, heterotetramer interface, or phosphorylation loop).6 No de novo observations, segregation data, same-residue pathogenic comparators, or functional studies were identified for this specific variant in the available evidence. Applying the VCEP framework: BS1 (Strong benign) is met based on population frequency exceeding the gene-specific threshold; PP3 (Supporting pathogenic) is met based on REVEL score >0.75. No other criteria are met. The strong benign criterion outweighs the single supporting pathogenic criterion.7

PP3 + BS1 VUS
Gene diagram · NM_001126131.1 · variants mapped to exon structure
POLG NM_001126131.1
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Absent from gnomAD v4.1.
      Overall AF
      53 / 282,776
      0.019%
      Highest · East Asian
      0.035%
      Homozygotes
      0
      grpmax FAF
      0.019%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 6 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      East Asian 7 / 19,954 0.035% 0
      European (non-Finnish) 36 / 129,110 0.028% 0
      South Asian 5 / 30,616 0.016% 0
      Remaining individuals 1 / 7,226 0.014% 0
      Admixed American 3 / 35,438 0.0085% 0
      African/African American 1 / 24,956 0.004% 0
      Ashkenazi Jewish 0 / 10,368
      European (Finnish) 0 / 25,108
      This variant is present in gnomAD v2.1 (AF= 0.000187428; MAF= 0.01874%, 53/282776 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000350807; MAF= 0.03508%, 7/19954 alleles, homozygotes = 0); grpmax FAF= 0.00018972.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (8 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 21313)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.915. BayesDel score = 0.512792.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. POLG, a mitochondrial DNA polymerase, is infrequently altered in cancers. Mutations in POLG are associated with inherited mitochondrial disorders, inc
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV51525791, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · 14 PMIDs triaged · 8 high-priority
      14papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      16401742 ↗ splicing rna
      Association of novel POLG mutations and multiple mitochondrial DNA deletions with variable clinical phenotypes in a Spanish population.
      Both dominant and recessive mutations were reported in the gene encoding the mitochondrial (mt) DNA polymerase gamma (POLG) in patients with progressive external ophthalmoplegia (PEO). Phenotypes other than PEO were recently documented in patients with mutations in the POLG gene. To screen patients with mitochondrial disease and multiple mtDNA deletions in muscle for mutations in the coding region
      BP7PP3PP5PS4PVS1
      20843780 ↗ functional
      Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing.
      A common goal in the discovery of rare functional DNA variants via medical resequencing is to incur a relatively lower proportion of false positive base-calls. We developed a novel statistical method for resequencing arrays (SRMA, sequence robust multi-array analysis) to increase the accuracy of detecting rare variants and reduce the costs in subsequent sequence verifications required in medical a
      BS3PP5PS3PS4
      21880868 ↗ functional
      Mitochondrial DNA polymerase gamma mutations: an ever expanding molecular and clinical spectrum.
      Mutations in the POLG gene have emerged as one of the most common causes of inherited mitochondrial diseases in children and adults. This study sequenced the exons and flanking intronic regions of the POLG gene from 2697 unrelated patients with clinical presentations suggestive of POLG deficiency. Informative mutations have been identified in 136 unrelated individuals (5%), including 92 patients w
      BS3PP5PS3PS4
      25462018 ↗ functional
      Polymorphisms in DNA polymerase γ affect the mtDNA stability and the NRTI-induced mitochondrial toxicity in Saccharomyces cerevisiae.
      Several pathological mutations have been identified in human POLG gene, encoding for the catalytic subunit of Pol γ, the solely mitochondrial replicase in animals and fungi. However, little is known regarding non-pathological polymorphisms found in this gene. Here we studied, in the yeast model Saccharomyces cerevisiae, eight human polymorphisms. We found that most of them are not neutral bu
      BS3PP5PS3PS4
      25741868 ↗ functional
      Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
      The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
      BS3PP5PS3PS4
      26467025 ↗ functional
      A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.
      We developed a rules-based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co-occurrence, segregation, and functional studies
      BS3PP5PS3PS4
      30838265 ↗ splicing rna
      Dystonia in a Patient with Autosomal-Dominant Progressive External Ophthalmoplegia Type 1 Caused by Mutation in the POLG Gene.
      BP7PP3PP5PS4PVS1
      32613234 ↗ functional
      The role of genetics in Parkinson's disease: a large cohort study in Chinese mainland population.
      This study aimed to determine the mutational spectrum of familial Parkinson's disease and sporadic early-onset Parkinson's disease (sEOPD) in a mainland Chinese population and the clinical features of mutation carriers. We performed multiplex ligation-dependent probe amplification assays and whole-exome sequencing for 1676 unrelated patients with Parkinson's disease in a mainland Chinese populatio
      BS3PP5PS3PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots