The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_024675.3(PALB2):c.3362del (p.Gly1121fs)

CA167019

126739 (ClinVar)

Gene: PALB2
Condition: hereditary breast cancer
Inheritance Mode: Autosomal dominant inheritance
UUID: d8eca774-205b-4826-8339-70e62b4579eb

HGVS expressions

NM_024675.3:c.3362delG
NM_024675.3(PALB2):c.3362del (p.Gly1121fs)
NC_000016.10:g.23603659del
CM000678.2:g.23603659del
NC_000016.9:g.23614980del
CM000678.1:g.23614980del
NC_000016.8:g.23522481del
NG_007406.1:g.42700del
ENST00000261584.9:c.3362del
ENST00000261584.8:c.3362del
ENST00000566069.5:n.128del
ENST00000568219.5:c.2477del
NM_024675.3:c.3362del
NM_024675.4:c.3362del
NM_024675.4(PALB2):c.3362del (p.Gly1121fs)

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 2
PVS1 PM5_Supporting
Not Met criteria codes 5
BA1 PP1 PM2 BS4 BS1

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.3362del (p.Gly1121fs) variant in PALB2 is a frameshift variant that may cause a premature stop codon that is predicted to escape nonsense mediated decay; however, it is a truncation of a functionally important region (removes amino acids 1123-1187) in a gene where loss-of-function is an established disease mechanism. This alteration results in a termination codon upstream of the most C-terminal pathogenic alteration (PALB2 p.Tyr1183*) as classified by the HBOP VCEP, and is expected to be more deleterious. This variant has a minor allele frequency in gnomAD v2.1.1 of 0.000003979 in the non-Finnish European population (PM2_Supporting, BS1, and BA1 are not met). In summary, this variant meets criteria to be classified likely 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)
Met criteria codes
PVS1
The c.3362del (p.Gly1121fs) variant in PALB2 is a frameshift variant that may cause a premature stop codon that is predicted to escape nonsense mediated decay; however, it is a truncation of a functionally important region (removes amino acids 1123-1187) in a gene where loss-of-function is an established disease mechanism (PVS1).
PM5_Supporting
This alteration results in a termination codon upstream of the most C-terminus pathogenic alteration (PALB2 p.Tyr1183*) as classified by the ClinGen HBOP Variant Curation Expert Panel, and is expected to be more deleterious (PM5_Supporting)
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
This variant has a Bayes factor of 0.751461 based on segregation across 19 families, which falls in the inconclusive range (0.49 to 2.1).
PM2
This variant has a minor allele frequency in gnomAD v2.1.1 of 0.0003979% in the non-Finnish European population (PM2_Supporting, BS1, and BA1 are not met).
BS4
This variant has a Bayes factor of 0.751461 based on segregation across 19 families, which falls in the inconclusive range (0.49 to 2.1).
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-04-05
Published on: 2023-04-07
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