rs515726117

Variant names:

• chr16-23603657-AC-A
• rs515726117
• NM_024675.4:c.3362delG

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM5_Supporting PVS1

This summary comes from the ClinGen Evidence Repository: 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) LINK:https://erepo.genome.network/evrepo/ui/classification/CA167019/MONDO:0016419/020

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000082 (0 hom.)
• Consequence: PALB2 NM_024675.4 frameshift
• Clinical Significance: Likely pathogenic reviewed by expert panel P:18
• Conservation: PhyloP100: 4.95

Genes affected

PALB2 (HGNC:26144): (partner and localizer of BRCA2) This gene encodes a protein that may function in tumor suppression. This protein binds to and colocalizes with the breast cancer 2 early onset protein (BRCA2) in nuclear foci and likely permits the stable intranuclear localization and accumulation of BRCA2. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PM5: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALB2	NM_024675.4	c.3362delG	p.Gly1121ValfsTer3	frameshift_variant	Exon 13 of 13	ENST00000261584.9	NP_078951.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALB2	ENST00000261584.9	c.3362delG	p.Gly1121ValfsTer3	frameshift_variant	Exon 13 of 13	1	NM_024675.4	ENSP00000261584.4

Frequencies

GnomAD3 genomes AF: 0.00000659 AC: 1 AN: 151828 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251320 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135870

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000880

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000821 AC: 12 AN: 1461832 Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5 AN XY: 727222

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000989

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000659 AC: 1 AN: 151828 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74118

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000113

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:18

Revision: reviewed by expert panel

Submissions by phenotype

Familial cancer of breast Pathogenic:9

Jan 11, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 13, 2019

Leiden Open Variation Database

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: curation

Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitter to LOVD: Marc Tischkowitz. -

Jun 01, 2015

Cancer Genetics Laboratory, Peter MacCallum Cancer Centre

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: case-control

- -

Sep 15, 2023

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. -

Jan 01, 2019

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 05, 2023

ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

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) -

Jan 26, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Gly1121Valfs*3) in the PALB2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 66 amino acid(s) of the PALB2 protein. This variant is present in population databases (rs515726117, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with breast cancer (PMID: 23935836, 24136930, 24549055, 25099575, 26283626; internal data). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 126739). This variant disrupts a region of the PALB2 protein in which other variant(s) (p.Leu1143Thrfs*14 and p.Tyr1183*) have been determined to be pathogenic (PMID: 17200668, 17200671, 21365267, 25099575, 25452441, 26315354; internal data). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Feb 23, 2022

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PVS1, PS3, PM2 -

Mar 23, 2022

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Gly1121ValfsX3 variant in PALB2 has been reported in at least 8 individuals with breast cancer, including 2 siblings with a family history of PALB2-associated cancers (Blanco 2013 PMID: 23935836, Janatova 2013 PMID: 24136930, Castera 2014 PMID: 24549055, Antoniou 2014 PMID: 25099575, Thompson 2015 PMID: 26283626, Couch 2015 PMID: 25452441, Lee 2018 PMID: 29431189) and has also been reported by other clinical laboratories in ClinVar (Variation ID 126739). It was identified in 0.001% (1/67996) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1). This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 1121 and leads to a premature termination codon 3 amino acids downstream. This alteration occurs within the last exon and is, therefore, likely to escape nonsense mediated decay (NMD) and result in a truncated protein that is missing ~5% of the coding region, with 62 amino acids removed. However, these terminal amino acids are part of the functionally critical WD40 domain that is necessary for PALB2 function, stability, and interaction with BRCA2 (Oliver 2009 PMID: 19609323). In addition, several downstream truncating variants, have been observed in individuals with PALB2-related cancers and Fanconi anemia, supporting the functional importance of the last exon. In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant PALB2-associated breast cancer. ACMG/AMP Criteria applied: PS4_Moderate, PM2_Supporting, PVS1_Strong. -

not provided Pathogenic:4

Dec 01, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The PALB2 c.3362del (p.Gly1121Valfs*3) variant alters the translational reading frame of the PALB2 mRNA and causes the premature termination of PALB2 protein synthesis. This variant has been reported in the published literature in individuals affected with breast cancer (PMIDs: 34399810 (2021), 32885271 (2021)), or prostate cancer (PMID: 32338768 (2020)). Functional evidence suggests that this variant may impact protein function(PMID: 31636395 (2020)). The frequency of this variant in the general population, 0.000013 (1/74796 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. -

Nov 03, 2021

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 27, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate a damaging effect: significantly reduced homology directed DNA repair functionality (Wiltshire et al., 2020); Frameshift variant predicted to result in protein truncation in a gene for which loss-of-function is a known mechanism of disease; Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 24870022, 29280214, 29431189, 29922827, 24136930, 25452441, 25099575, 24549055, 26283626, 28454591, 31447099, 32338768, 32853339, 34399810, 33804961, 23935836, 31636395) -

Dec 08, 2020

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

DNA sequence analysis of the PALB2 gene demonstrated a single base pair deletion in exon 13, c.3362del. This sequence change is predicted to result in an amino acid frameshift and the creation of a premature stop codon 2 amino acids downstream of the mutation, p.Gly1121Valfs*3. Although this sequence change is located in the last exon of the PALB2 gene, another truncating variant downstream of the p.Gly1121Valfs*3 change, p.Tyr1183*, has been described in individuals with PALB2-related disorders and has been classified as pathogenic (PMID: 17200668, 17200671, 21365267, 25099575, 25452441, 26315354). The p.Gly1121Valfs*3 change is predicted to result in an abnormal transcript, which may be degraded, or may lead to the production of a truncated PALB2 protein with potentially abnormal function. This sequence change has been described in the gnomAD database in one individual with an overall population frequency of 0.0004% (dbSNP rs515726117). The p.Gly1121Valfs*3 change has been described in several individuals with breast cancer (PMIDs: 23935836, 26283626, 24136930, 24549055, 25099575, 26283626). This sequence change is located in the WD40-repeat domain of the PALB2 protein, which is known to be involved in binding with BRCA2 (PMIDs: 16793542, 19423707). These collective evidences suggest that this sequence change is pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Dec 14, 2022

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant deletes 1 nucleotide in exon 13 of the PALB2 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in at least eight individuals affected with breast, ovarian and pancreatic cancer (PMID: 23935836, 24136930, 24549055, 25452441, 29431189, Color internal data). This variant has been identified in 1/251320 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of PALB2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Jan 24, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.3362delG pathogenic mutation, located in coding exon 13 of the PALB2 gene, results from a deletion of one nucleotide at nucleotide position 3362, causing a translational frameshift with a predicted alternate stop codon (p.G1121Vfs*3). This alteration occurs at the 3' terminus of thePALB2 gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 66 amino acids of the protein. However, premature stop codons are typically deleterious in nature and the impacted region is critical for protein function (Ambry internal data). This mutation has been previously reported in numerous kindreds characterized by early-onset breast cancer, triple negative breast cancer, prostate and/or pancreatic cancer (Blanco A at al. PLoS ONE. 2013 Jul;8:e67538; Janatova M et al. Cancer Epidemiol. Biomarkers Prev. 2013 Dec;22:2323-32; Antoniou AC et al. N. Engl. J. Med. 2014 Aug;371:497-506; Castéra L et al. Eur. J. Hum. Genet. 2014 Nov;22:1305-13; Couch FJ et al. J. Clin. Oncol. 2015 Feb;33:304-11; Thompson ER et al. Breast Cancer Res. 2015 Aug;17:111; Thompson ER et al. J Clin Oncol, 2016 May;34:1455-9; Lee JEA et al. J. Pathol. 2018 May;245(1):53-60; Nguyen-Dumont T et al. Int J Cancer, 2020 10;147:2142-2149). This alteration was found to be functionally abnormal in a homology-directed DNA repair (HDR) assay (Wiltshire T et al. Genet Med, 2020 03;22:622-632). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Breast and/or ovarian cancer Pathogenic:1

Mar 30, 2020

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Malignant tumor of breast Pathogenic:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The PALB2 p.Gly1121Valfs*3 variant was identified in 7 of 9236 proband chromosomes (frequency: 0.0008) from individuals or families with hereditary breast and ovarian cancer or pancreatic cancer (Antoniou 2014, Blanco 2013, Castera 2014, Couch 2015, Thompson 2015, Janatova 2013, Johns 2017). The variant was identified in dbSNP (ID: rs515726117 as “With Pathogenic allele”), ClinVar (5x as pathogenic by Ambry Genetics, Invitae, GeneDx, Color Genomics and PALB2 database and 1x as likely pathogenic by Peter MacCallum Cancer Centre), and LOVD 3.0 Database (5x). The variant was not identified in Cosmic, MutDB, or the Zhejiang University Database. The variant was identified in control databases in 1 of 246142 chromosomes at a frequency of 0.000004 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the European (Non-Finnish) population in 1 of 111636 chromosomes (freq: 0.000009), but not in the other populations. The p.Gly1121Valfs*3 variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 1121 and leads to a premature stop codon at position 1123. This alteration is predicted to result in a truncated protein and loss of function. Loss of function variants of the PALB2 gene are an established mechanism of disease in hereditary breast and ovarian cancer and is the type of variant expected to cause the disorder. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. -

Hereditary breast ovarian cancer syndrome Pathogenic:1

Oct 31, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: PALB2 c.3362delG (p.Gly1121ValfsX3) results in a premature termination codon, predicted to cause a truncation of the encoded protein, however, nonsense mediated decay is not expected to occur. The variant disrupts the Partner and localiser of BRCA2, WD40 domain which is involved in BRCA2 binding. A truncation downstream of this position has been classified as pathogenic by our laboratory (e.g. p.Tyr1183X). The variant allele was found at a frequency of 4.1e-06 in 246142 control chromosomes. c.3362delG has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (e.g. Blanco_2013, Couch_2016, Janatova_2013, Thompson_2015). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 25452441, 23935836, 26283626, 26057125). ClinVar contains an entry for this variant (Variation ID: 126739). Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs515726117; hg19: chr16-23614978;