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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 applied · 14 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PP3 supporting Pathogenic
The REVEL in silico predictor score of 0.915 exceeds the VCEP-specified threshold of >0.75 for PP3 at Supporting strength, indicating multiple lines of computational evidence support a deleterious effect.
REVEL score = 0.915. VCEP PP3 threshold: REVEL >0.75 (Supporting). BayesDel score = 0.513 (supportive but not independently applied per VCEP). SpliceAI max delta = 0.00 (no splicing impact).
BS1 strong Benign
The variant is present in gnomAD v2.1 at an overall allele frequency of 0.01874% (53/282,776 alleles) with a maximum subpopulation frequency of 0.03508% in East Asians, which exceeds the POLG VCEP BS1 threshold of >0.0092%.
gnomAD v2.1: overall AF=0.01874% (53/282776 alleles0 homozygotes)
Assessed · not applied
Pathogenic
PS1 No evidence of a different nucleotide change at codon 1146 resulting in the same amino acid change (p.Arg1146Cys) that has been established as pathogenic.
PS2 No de novo observation for this variant has been reported in any of the available evidence sources or publications.
PM1 Amino acid position 1146 (Arg1146) is not located within any of the POLG functional domains specified by the VCEP: TPP binding site, alpha-beta heterodimer interface, alpha2-beta2 heterotetramer interface, or phosphorylation loop region.
PM2 The variant is present in gnomAD v2.1 at an allele frequency of 0.01874% (53/282,776 alleles), which exceeds the POLG VCEP PM2 threshold of <0.00092%.
PM5 No pathogenic missense variants at amino acid position 1146 other than p.Arg1146Cys were identified in ClinVar or the literature.
PM6 No de novo observation (confirmed or assumed) for this variant has been reported in any available evidence source or publication.
PP1 No co-segregation data is available for this variant.
PP4 No patient phenotype data is available for this adjudication.
Benign
BA1 The maximum population allele frequency of 0.03508% (gnomAD v2.1 East Asian) is below the POLG VCEP BA1 threshold of >0.092%.
BS2 No homozygous individuals are observed in gnomAD (0 homozygotes across 282,776 alleles in v2.1; absent in v4.1).
BS4 No segregation data is available for this variant.
BP2 No evidence of the variant being observed in trans with a pathogenic variant or in cis with a pathogenic variant has been reported.
BP4 The REVEL score of 0.915 far exceeds the VCEP BP4 threshold of <0.15.
BP5 No evidence has been identified of this variant being found in a case with an alternate molecular basis for disease.
N/A · 10 PVS1 · PS3 · PS4 · PP2 · PP5 · BS3 · BP1 · BP3 · BP6 · BP7
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 &#x3b3; 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