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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
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      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.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      0.019% · 53 / 282,776
      0 hom · FAF 0.019%
      East Asian
      7 / 19,954
      0.035%
      European (non-Finnish)
      36 / 129,110
      0.028%
      South Asian
      5 / 30,616
      0.016%
      Remaining individuals
      1 / 7,226
      0.014%
      Admixed American
      3 / 35,438
      0.0085%
      African/African American
      1 / 24,956
      0.004%
      + 2 not observed (Ashkenazi Jewish, European (Finnish))
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      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.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      16401742 ↗ Association of novel POLG mutations and multiple mitochondrial DNA deletions with variable clinical phenotypes in a Spanish population. CLINVAR
      20843780 ↗ Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. CLINVAR
      21880868 ↗ Mitochondrial DNA polymerase gamma mutations: an ever expanding molecular and clinical spectrum. CLINVAR
      25462018 ↗ Polymorphisms in DNA polymerase γ affect the mtDNA stability and the NRTI-induced mitochondrial toxicity in Saccharomyces cerevisiae. CLINVAR
      25741868 ↗ 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. CLINVAR
      26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR
      30838265 ↗ Dystonia in a Patient with Autosomal-Dominant Progressive External Ophthalmoplegia Type 1 Caused by Mutation in the POLG Gene. CLINVAR
      32613234 ↗ The role of genetics in Parkinson's disease: a large cohort study in Chinese mainland population. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR