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Variant: NM_024675.3(PALB2):c.3249G>C (p.Glu1083Asp)

CA288472

126726 (ClinVar)

Gene: PALB2
Condition: hereditary breast cancer
Inheritance Mode: Autosomal dominant inheritance
UUID: 27b045d7-68a2-4cb4-b7f9-e2837a29e462
Approved on: 2023-04-05
Published on: 2023-04-07

HGVS expressions

NM_024675.3:c.3249G>C
NM_024675.3(PALB2):c.3249G>C (p.Glu1083Asp)
NC_000016.10:g.23607965C>G
CM000678.2:g.23607965C>G
NC_000016.9:g.23619286C>G
CM000678.1:g.23619286C>G
NC_000016.8:g.23526787C>G
NG_007406.1:g.38393G>C
ENST00000261584.9:c.3249G>C
ENST00000261584.8:c.3249G>C
ENST00000566069.5:n.117-4296G>C
ENST00000568219.5:c.2364G>C
NM_024675.4:c.3249G>C
NM_024675.4(PALB2):c.3249G>C (p.Glu1083Asp)
More

Benign

Met criteria codes 1
BA1
Not Met criteria codes 6
PP3 PM2 BS1 BS3 BS2 BP4

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.3249G>C (p.Glu1083Asp) variant in PALB2 is a missense variant predicted to cause substitution of glutamic acid by aspartic acid at amino acid 1083 (p.Glu1083Asp). This variant has a gnomAD v2.1.1 filtering allele frequency of 0.001331 in the Latino/Admixed American population, which is higher than the HBOP VCEP threshold (>0.001) for BA1, and therefore meets this criterion. This variant is functional in multiple protein assays; however, due to a lack of positive missense controls with known clinical impact, these assays do not meet the requirements for use by the HBOP VCEP (PMID: 31636395). PALB2, in which the variant was identified, is defined by the HBOP VCEP as a gene for which primarily truncating variants are known to cause disease. In summary, this variant meets the criteria to be classified as benign 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. (BA1, BP1)
Met criteria codes
BA1
The highest population filtering allele frequency in gnomAD v2.1.1 is 0.001331 in Latino/Admixed American population, which is higher than the ClinGen Hereditary Breast, Ovarian, and Pancreatic Cancer VCEP threshold (>0.001) for BA1, and therefore meets this criterion (BA1).
Not Met criteria codes
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
A homology-directed repair (HDR) protein assay in mouse mammary tumor cell line B400 (Palb2-/-; Trp53-/-) showed no significant change in HDR (5.1 fold change in HDR compared to 5.0 fold change in HDR for wild type PALB2) indicating that this variant does not impact protein function (PMID: 31636395); however, due to a lack of positive missense controls with known clinical impact, this assay does not meet the requirements for use by the HBOP VCEP.
BS2
This variant has been observed in combination with a second PALB2 variant, c.2167_2168delAT, which has not yet been classified by the ClinGen HBOP VCEP, in an unaffected adult individual over 40 years of age (Ambry). The phase of the variants was not confirmed (0.5 points). Evidence from this occurrence is not sufficient to apply BS2.
BP4
The computational splicing predictor SpliceAI gives scores of AL: 0.00/DL: 0.00/AG: 0.20/DG: 0.00, suggesting that the variant has no impact on splicing. However, BP4 was not met since this variant has a putative protein effect.
Curation History
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