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PPM1D
Final classification
Likely Pathogenic
PS3PM1PM2
PPM1D
c.1473dup
p.Asn492Ter
This variant

NM_003620.3:c.1473dupT (p.Asn492Ter) is a nonsense variant in exon 6 of PPM1D that truncates the protein within the C-terminal degradation domain.

Transcript
NM_003620.3
HGVS · transcript:coding
NM_003620.3:c.1473dup
GRCh38
chr17:60663206 A>AT
GRCh37
chr17:58740567 A>AT
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: PS3 strong, PM1 moderate, PM2 supporting; combination = 1 strong + 1 moderate + 1 supporting, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PM1 moderate, PM2 supporting; combination = 1 strong + 1 moderate + 1 supporting, which maps to Likely Pathogenic.
Classification rationale
PS3PM1PM2 Likely Pathogenic
PPM1D c.1473dup

NM_003620.3:c.1473dupT (p.Asn492Ter) is a nonsense variant in exon 6 of PPM1D that truncates the protein within the C-terminal degradation domain. This variant is absent from gnomAD v4.1 (0/1,614,190 alleles), satisfying PM2 at supporting level.1 Functional evidence from a CRISPR-Cas9 tiling screen demonstrates that truncating mutations in the PPM1D exon 6 region (amino acids 400-585, encompassing N492) confer chemoresistance and selective advantage through a gain-of-function mechanism (PMID:29954749).2 Multiple independent studies confirm that exon 6 truncating PPM1D mutations produce a hyperstable protein with enhanced phosphatase activity due to loss of the C-terminal degradation domain (PMID:24880341, PMID:25742468, PMID:23907125).3 OncoKB classifies p.N492* as Likely Oncogenic with Likely Gain-of-function biological effect.4 PVS1 is not met because truncating PPM1D exon 6 mutations are gain-of-function, not loss-of-function; the variant produces a hyperstable, hyperactive protein rather than a null allele.5 PM1 is met at moderate level: p.Asn492Ter removes the C-terminal degradation domain, a critical regulatory region whose loss is functionally characterized across multiple studies.6 Overall classification: Likely Pathogenic based on PS3 (strong), PM1 (moderate), and PM2 (supporting) according to ACMG/AMP 2015 combination rules (1 strong + 1 moderate).7

PS3 + PM1 + PM2 Likely Pathogenic
Gene diagram · NM_003620.3 · variants mapped to exon structure
PPM1D NM_003620.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 13 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 3
Strength Supporting Moderate Strong Very strong
PS3 strong Pathogenic
The variant p.Asn492Ter falls within the C-terminal degradation domain (amino acids ~400-605) of PPM1D that has been systematically characterized as a gain-of-function region by a CRISPR-Cas9 tiling screen (PMID:29954749, 265 gRNAs spanning the entire protein-coding region). This screen demonstrated that truncating mutations in amino acids 400-585 confer chemoresistance and selective advantage under DNA-damaging agents. Multiple independent publications confirm the gain-of-function mechanism: exon 6 truncating mutations produce a hyperstable protein with enhanced phosphatase activity that suppresses p53 and CHK2 phosphorylation (PMID:24880341, PMID:25742468, PMID:23907125). The variant is functionally characterized within a systematically tested range in >=2 independent publications.
CRISPR-Cas9 tiling screen (265 gRNAs across PPM1D) in PMID:29954749 shows truncating mutations in aa 400-585 confer chemoresistanceN492 falls within this systematically characterized rangePMID:24880341 demonstrates exon 6 truncating mutations enhance ability to suppress Chk2 phosphorylation (gain-of-function)
PM1 moderate Pathogenic
p.Asn492Ter truncates the protein within the well-characterized C-terminal degradation domain of PPM1D (exon 6, approximately amino acids 400-605). This domain is established as a critical regulatory region in multiple publications: its loss results in a hyperstable protein with enhanced phosphatase activity due to impaired proteasomal degradation (PMID:29954749, PMID:25742468, PMID:23907125). The truncation removes this functionally characterized degradation domain, consistent with the domain-level application of PM1.
Variant truncates PPM1D within the C-terminal degradation domain (exon 6aa ~400-605)Loss of this domain results in hyperstable protein with enhanced phosphatase activity (PMID:29954749)
PM2 supporting Pathogenic
NM_003620.3:c.1473dupT is absent from gnomAD v4.1 (0/1,614,190 alleles) and gnomAD v2.1. Under generic ACMG/AMP, allele frequency below 0.1% in population databases supports PM2 at supporting level.
Absent from gnomAD v4.1 (0/1614190 alleles
Assessed · not applied · 13 not met · 0 not assessed
Pathogenic
PVS1 While NM_003620.3:c.1473dupT (p.Asn492Ter) is a nonsense variant predicted to truncate the protein, truncating mutations in exon 6 of PPM1D are functionally characterized as gain-of-function, not loss-of-function.
PS2 No de novo report for NM_003620.3:c.1473dupT was identified in any publication reviewed.
PS4 No case-control study or significant enrichment data for NM_003620.3:c.1473dupT was identified in the reviewed literature.
PP1 No segregation data for NM_003620.3:c.1473dupT was identified in any reviewed publication.
PP3 SpliceAI predicts no significant splice impact (max delta score = 0.00).
PP4 No specific phenotype or clinical data for the proband carrying NM_003620.3:c.1473dupT was available for review.
PP5 NM_003620.3:c.1473dupT is absent from ClinVar; no reputable source has classified this variant as pathogenic.
Benign
BA1 Variant is absent from gnomAD (0/1,614,190 alleles).
BS1 Variant is absent from gnomAD (0/1,614,190 alleles).
BS3 No benign functional studies for NM_003620.3:c.1473dupT were identified.
BP3 Not an in-frame deletion/insertion in a repetitive region without known function.
BP4 SpliceAI max delta score = 0.00, indicating no predicted splice impact.
BP7 Not a synonymous variant.
N/A · 12 PS1 · PM3 · PM4 · PM5 · PM6 · PP2 · BS2 · BS4 · BP1 · BP2 · BP5 · BP6
Research & evidence
Population frequency · supports pathogenic
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= 0; MAF= 0.00000%, 0/1614190 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/75058 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / 1,614,190
0 hom
Not observed in any ancestry group.
+ 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
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.
Literature · how each cited paper was used
3papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 2 further PMIDs triaged but not cited — see Sources & references.
Rule & framework references · cited for criterion definitions, not variant evidence
24880341 ↗ Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas.
25742468 ↗ Truncating mutations of PPM1D are found in blood DNA samples of lung cancer patients.
29954749 ↗ PPM1D-truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 2 PMIDs not cited in assessment
23907125 ↗ Genetic variants and mutations of PPM1D control the response to DNA damage. ONCOKB
30304655 ↗ Classification and Personalized Prognosis in Myeloproliferative Neoplasms. ONCOKB