The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data


Variant: NM_024675.3(PALB2):c.514_517del (p.Ser172fs)

CA658658444

461007 (ClinVar)

Gene: PALB2
Condition: hereditary breast cancer
Inheritance Mode: Autosomal dominant inheritance
UUID: 91b89b30-550a-4e79-8b26-8385707c9d23
Approved on: 2023-04-05
Published on: 2023-04-07

HGVS expressions

NM_024675.3:c.514_517del
NM_024675.3:c.514_517delTCTG
NM_024675.3(PALB2):c.514_517del (p.Ser172fs)
NC_000016.10:g.23636031_23636034del
CM000678.2:g.23636031_23636034del
NC_000016.9:g.23647352_23647355del
CM000678.1:g.23647352_23647355del
NC_000016.8:g.23554853_23554856del
NG_007406.1:g.10326_10329del
ENST00000561514.3:c.520_523del
ENST00000565038.2:c.211+1818_211+1821del
ENST00000566069.6:c.514_517del
ENST00000697377.2:c.520_523del
ENST00000697379.2:c.520_523del
ENST00000561514.2:c.-372_-369del
ENST00000697374.1:c.-372_-369del
ENST00000697375.1:n.1861_1864del
ENST00000697376.1:c.-372_-369del
ENST00000697377.1:c.-372_-369del
ENST00000697378.1:n.1034_1037del
ENST00000697379.1:c.-372_-369del
ENST00000697382.1:c.-372_-369del
ENST00000697383.1:c.48+5078_48+5081del
ENST00000697384.1:n.668_671del
ENST00000261584.9:c.514_517del
ENST00000261584.8:c.514_517del
ENST00000565038.1:c.86+1818_86+1821del
ENST00000568219.5:c.-372_-369del
NM_024675.4:c.514_517del
More

Pathogenic

Met criteria codes 4
PM5_Supporting PVS1 PM2_Supporting PP1_Moderate

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PALB2 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Breast, Ovarian and Pancreatic Cancer VCEP
The c.514_517del (p.Ser172fs) variant in PALB2 is a frameshift variant predicted to result in nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism. This alteration results in a termination codon upstream of the most C-terminus pathogenic alteration (PALB2 p.Tyr1183*), as classified by the HBOP VCEP, and is expected to be more deleterious. This variant is absent from gnomAD v2.1.1. This variant was found to co-segregate with disease in multiple affected family members in one family (Invitae). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant hereditary breast and pancreatic cancer and autosomal recessive FANCN based on the ACMG/AMP criteria applied, as specified by the HBOP VCEP. (PVS1, PM5_Supporting, PM2_Supporting, PP1_Moderate)
Met criteria codes
PM5_Supporting
This alteration results in a termination codon upstream of the most C-terminus pathogenic alteration (PALB2 c.3549C>A (p.Tyr1183Ter)), as classified by the ClinGen Hereditary Breast, Ovarian, and Pancreatic Cancer VCEP, and is expected to be more deleterious (PM5_Supporting)
PVS1
The c.514_517del (p.Ser172fs) variant is predicted to result in a premature stop codon that leads to truncated or absent protein (PVS1)
PM2_Supporting
Variant is absent in the GnomAD cohort (PM2_Supporting)
PP1_Moderate
Co-segregation with breast cancer in multiple affected family members with LOD ≥.60 or Bayes Factor (LR) ≥4:1 (ClinVar/GTR LabID: 500031) (PP1_Moderate).
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.