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PPM1D
Final classification
VUS
PPM1D c.1525G>C · p.Asp509His
PPM1D

NM_003620.3:c.1525G>C (p.Asp509His) is a missense variant in exon 6 of PPM1D that is absent from gnomAD v2.1 and present at very low frequency in gnomAD v4.1 (AF = 0.0086%, 139/1,613,978 alleles, 0 homozygotes; grpmax FAF = 0.0096%), meeting PM2 at supporting level.

Gene
PPM1D
Transcript
NM_003620.3
HGVS · transcript:coding
NM_003620.3:c.1525G>C
Consequence
N/A
GRCh38
chr17:60663259 G>C
GRCh37
chr17:58740620 G>C
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
PPM1D c.1525G>C

NM_003620.3:c.1525G>C (p.Asp509His) is a missense variant in exon 6 of PPM1D that is absent from gnomAD v2.1 and present at very low frequency in gnomAD v4.1 (AF = 0.0086%, 139/1,613,978 alleles, 0 homozygotes; grpmax FAF = 0.0096%), meeting PM2 at supporting level.1 Multiple lines of in silico evidence suggest a benign effect: REVEL score 0.325 (benign range), BayesDel score 0.081 (tolerated), and SpliceAI max delta 0.00 (no predicted splice impact), meeting BP4 at supporting benign level.2 This variant has been reported in ClinVar as Likely benign by a single clinical laboratory (Labcorp/Invitae, 1-star, criteria provided, single submitter). This does not reach the 3-star expert panel threshold for PP5 or BP6 application.3 No variant-specific functional studies, segregation data, de novo observations, or case-control data were identified for this variant. OncoKB reports Unknown Oncogenic Effect with no variant-specific functional evidence.4 The variant has not been reported in COSMIC and does not lie in a statistically significant mutational hotspot per cancerhotspots.org. Using generic ACMG/AMP 2015 combination rules (PMID:25741868): PM2 (supporting) and BP4 (supporting benign) are opposing and cancel. No criteria combination threshold for pathogenic, likely pathogenic, benign, or likely benign is reached. This variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_003620.3 · variants mapped to exon structure
PPM1D NM_003620.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_003620.3:c.1525G>C is absent from gnomAD v2.1 and present at very low frequency in gnomAD v4.1 (overall AF = 0.0086%, 139/1,613,978 alleles, 0 homozygotes; grpmax FAF = 9.607e-05). This is well below the 0.1% PM2 threshold for a rare variant.
Absent from gnomAD v2.1.gnomAD v4.1: AF = 0.0086% (139/1613
BP4 supporting Benign
Multiple lines of computational evidence support a benign effect: REVEL score 0.325 (below 0.5 pathogenic threshold), BayesDel score 0.081 (well below damaging threshold), and SpliceAI max delta score 0.00 (no predicted splicing impact). Three independent in silico tools consistently predict a tolerated/benign effect.
REVEL: 0.325 (tolerated/benign range).BayesDel: 0.081 (tolerated).SpliceAI: delta 0.00 (no splice alteration).
Assessed · not applied
Pathogenic
PS1 No prior observation of a pathogenic variant resulting in the same amino acid change (p.Asp509His or p.D509H) was identified in ClinVar, literature, or other curated databases.
PS2 No de novo observation with confirmed parentage was identified for this variant in the available literature or databases.
PS3 No variant-specific functional studies testing NM_003620.3:c.1525G>C (p.Asp509His) were identified.
PS4 No case-control or cohort enrichment data comparing affected versus control populations was identified for this variant.
PM1 Residue D509 is not a statistically significant mutational hotspot per cancerhotspots.org.
PM5 No same-residue (D509) alternative pathogenic missense variant was identified.
PM6 No de novo observation (with or without confirmed parentage) was identified for this variant.
PP1 No cosegregation data with disease in affected family members was identified for this variant.
PP2 HCI prior probability is not available for PPM1D.
PP3 Multiple in silico tools predict a benign or tolerated effect: REVEL score 0.325 (below 0.5 threshold), BayesDel score 0.081 (well below damaging threshold), and SpliceAI max delta 0.00 (no predicted splice impact).
PP4 No phenotype or family history data specific to a PPM1D-associated disorder was available for the proband harboring this variant.
PP5 ClinVar reports this variant as Likely benign (1-star, criteria provided, single submitter).
Benign
BA1 gnomAD v4.1 allele frequency is 0.0086%, well below the 1% BA1 threshold.
BS1 gnomAD v4.1 allele frequency is 0.0086%, well below the 0.3% BS1 threshold for a rare variant being too common for a fully penetrant disorder.
BS2 No data available on observation of this variant in healthy adults at an age where full penetrance of a PPM1D-associated disorder would be expected.
BS3 No variant-specific functional studies demonstrating a benign effect for NM_003620.3:c.1525G>C were identified in the literature or curated databases.
BS4 No nonsegregation data (variant absent in affected family members) was available for this variant.
BP1 While PPM1D truncating variants are associated with cancer predisposition, missense variants in PPM1D have also been reported as potentially disease-associated (e.g., c.1607G>A, p.Arg536Lys in PMID:27401275).
BP2 No observation of this variant in trans with a known pathogenic PPM1D variant was identified.
BP5 No observation of this variant in a case where an alternate molecular basis for disease was identified was available.
BP6 ClinVar reports this variant as Likely benign (1-star, criteria provided, single submitter — Labcorp/Invitae).
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 8.61226e-05; MAF= 0.00861%, 139/1613978 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000111862; MAF= 0.01119%, 132/1180030 alleles, homozygotes = 0); grpmax FAF= 9.607e-05.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0086% · 139 / 1,613,978
0 hom · FAF 0.0096%
European (non-Finnish)
132 / 1,180,030
0.011%
Admixed American
3 / 59,982
0.005%
Remaining individuals
3 / 62,480
0.0048%
African/African American
1 / 74,900
0.0013%
+ 6 not observed (European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Likely benign (1 clinical laboratory). (ClinVarID = 2170443)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.325. BayesDel score = 0.0808168.
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. PPM1D, a protein phosphatase, is altered by mutation in various solid and hematologic malignancies including in therapy-related hematopoietic disorder
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 not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 1 PMID not cited in assessment
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR