Starting
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PALB2
Final classification
Pathogenic
PALB2 c.509_510del · p.Arg170IlefsTer14
PALB2

NM_024675.4:c.509_510delGA (p.Arg170IlefsTer14) is a frameshift deletion in exon 4 of PALB2 that introduces a premature termination codon at position 184, predicted to undergo nonsense-mediated decay and resulting in loss of all C-terminal functional domains including the WD40 repeat/BRCA2-binding region. Loss of function is an established disease mechanism for PALB2 (PVS1_Strong).

Gene
PALB2
Transcript
NM_024675.4
HGVS · transcript:coding
NM_024675.4:c.509_510del
Consequence
N/A
GRCh38
chr16:23636035 ATC>A
GRCh37
chr16:23647356 ATC>A
Basis Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule5 (Pathogenic.Strong >=2) with applied criteria: PVS1 strong, PS4 strong, PM5 supporting; maps to Pathogenic.
Richards et.al., 2015 - Combining rules v1.2.0 criteria-combination framework: matched Rule5 (Pathogenic.Strong >=2) with applied criteria: PVS1 strong, PS4 strong, PM5 supporting; maps to Pathogenic.
Classification rationale
PVS1PS4PM5 Pathogenic
PALB2 c.509_510del

NM_024675.4:c.509_510delGA (p.Arg170IlefsTer14) is a frameshift deletion in exon 4 of PALB2 that introduces a premature termination codon at position 184, predicted to undergo nonsense-mediated decay and resulting in loss of all C-terminal functional domains including the WD40 repeat/BRCA2-binding region. Loss of function is an established disease mechanism for PALB2 (PVS1_Strong).1 The variant is significantly enriched in breast cancer cases compared to population controls. Noskowicz et al. (2014) identified the variant in 10/3,924 (0.25%) unselected breast cancer patients from Central/Eastern Europe versus 0/2,827 healthy controls (p=0.007). Additional studies corroborate this enrichment: Dansonka-Mieszkowska et al. (2010) found the variant in 6/987 (0.6%) cancer cases versus 1/1,310 controls; Kluska et al. (2017) detected it in 0.5% of 807 BRCA1/2-negative breast/ovarian cancer patients; and Bogdanova et al. (2011) identified it in 2/203 bilateral breast cancer patients. Collectively, these studies meet PS4 at Strong strength.2 The premature termination codon at position 184 lies upstream of p.Tyr1183, the most C-terminal known pathogenic variant in PALB2, consistent with loss of critical functional domains. Under the PALB2 VCEP, this satisfies PM5_Supporting. The variant is present at low frequency in gnomAD (v4.1: 30/1,614,006, 0.00186%; v2.1: 9/251,446, 0.00358%), with no homozygotes. This frequency exceeds the PALB2 VCEP PM2_Supporting threshold (≤0.000333%) and remains well below benign population thresholds (BA1 >0.1%, BS1 >0.01%), providing neither pathogenic nor benign population evidence.3 SpliceAI predicts no cryptic splice effect (max delta = 0.00). No co-segregation or non-segregation data are available. No functional studies specific to this variant have been published.4

PVS1 + PS4 + PM5 Pathogenic
1 pvs1_gene_contextpvs1_variant_assessment
Gene diagram · NM_024675.4 · variants mapped to exon structure
PALB2 NM_024675.4
Fetching transcript structure from UCSC…
Applied criteria · 3 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 · 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= 1.85873e-05; MAF= 0.00186%, 30/1614006 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.45759e-05; MAF= 0.00246%, 29/1180016 alleles, homozygotes = 0); grpmax FAF= 1.724e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.5793e-05; MAF= 0.00358%, 9/251446 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.00016292; MAF= 0.01629%, 1/6138 alleles, homozygotes = 0); grpmax FAF= 3.419e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0019% · 30 / 1,614,006
      0 hom · FAF 0.0017%
      European (non-Finnish)
      29 / 1,180,016
      0.0025%
      Remaining individuals
      1 / 62,488
      0.0016%
      + 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0036% · 9 / 251,446
      0 hom · FAF 0.0034%
      Remaining individuals
      1 / 6,138
      0.016%
      European (non-Finnish)
      8 / 113,732
      0.007%
      + 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (49 clinical laboratories) and as pathogenic (1 clinical laboratory). (ClinVarID = 126757)
      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 Loss-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 previously been reported in somatic cancers (COSMIC; COSV108015612, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      4papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & References.
      A novel germline PALB2 deletion in Polish breast and ovarian cancer patients.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS4 supports · met
      PMID 24061862
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS4 supports · met
      PALB2 mutations in BRCA1/2-mutation negative breast and ovarian cancer patients from Poland.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS4 supports · met
      PMID 31312277
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS4 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 7 PMIDs not cited in assessment
      18053174 ↗ Identification of a novel truncating PALB2 mutation and analysis of its contribution to early-onset breast cancer in French-Canadian women. ONCOKB
      25529982 ↗ A novel PALB2 truncating mutation in an Italian family with male breast cancer. ONCOKB
      28779002 ↗ Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. ONCOKB
      28858227 ↗ The Role of PALB2 in the DNA Damage Response and Cancer Predisposition. ONCOKB
      29484706 ↗ Identification of a novel truncating mutation in PALB2 gene by a multigene sequencing panel for mutational screening of breast cancer risk-associated and related genes. ONCOKB
      17200671 ↗ Biallelic mutations in PALB2 cause Fanconi anemia subtype FA-N and predispose to childhood cancer. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR