NM_024675.4(PALB2):c.509_510del (p.Arg170fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (6 submissions)
Last evaluated:: Mar 6, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000130658.26

Allele description [Variation Report for NM_024675.4(PALB2):c.509_510del (p.Arg170fs)]

NM_024675.4(PALB2):c.509_510del (p.Arg170fs)

Gene:

PALB2:partner and localizer of BRCA2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p12.2

Genomic location:

Preferred name:

NM_024675.4(PALB2):c.509_510del (p.Arg170fs)

HGVS:

NC_000016.10:g.23636037_23636038del
NG_007406.1:g.10321_10322del
NM_024675.4:c.509_510delMANE SELECT
NP_078951.2:p.Arg170fs
LRG_308:g.10321_10322del
NC_000016.10:g.23636036_23636037delTC
NC_000016.9:g.23647357_23647358del
NC_000016.9:g.23647358_23647359del
NC_000016.9:g.23647358_23647359delCT
NM_024675.3:c.509_510delGA
NM_024675.4:c.509_510delGAMANE SELECT
p.Arg170Ilefs*14
p.R170IFS*14
p.R170IfsX14

Links:

dbSNP: rs515726123

NCBI 1000 Genomes Browser:

rs515726123

Molecular consequence:

NM_024675.4:c.509_510del - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Bovine viral diarrhea virus partial 5'UTR region, genotype BVDV1a, strain MRI226...
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000185544	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Oct 26, 2021)	germline	clinical testing	PubMed (16) [See all records that cite these PMIDs] 20122277, 20412113, 20582465, 21165770, 21285249, 21365267, 24061862, 25330149, 25959805, 26270727, 26720728, 27038244, 27099641, 27106063, 28158555, 28279176 Citation Link,
SCV000266111	University of Washington Department of Laboratory Medicine, University of Washington	criteria provided, single submitter (Shirts et al. (Genet Med 2016))	Pathogenic (Nov 20, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000686065	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 6, 2023)	germline	clinical testing	PubMed (13) [See all records that cite these PMIDs] 20122277, 20412113, 20582465, 21285249, 24061862, 24136930, 25099575, 25186627, 26270727, 27106063, 28158555, 33471991, 25741868
SCV000821754	GeneKor MSA	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 1, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000839054	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Pathogenic (Jul 2, 2018)	unknown	clinical testing	Citation Link,
SCV002819235	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 22, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

PALB2 mutations in German and Russian patients with bilateral breast cancer.

Bogdanova N, Sokolenko AP, Iyevleva AG, Abysheva SN, Blaut M, Bremer M, Christiansen H, Rave-Fränk M, Dörk T, Imyanitov EN.

Breast Cancer Res Treat. 2011 Apr;126(2):545-50. doi: 10.1007/s10549-010-1290-4. Epub 2010 Dec 17.

PubMed [citation]

PMID:: 21165770
PMCID:: PMC3291835

PALB2 mutations in familial breast and pancreatic cancer.

Hofstatter EW, Domchek SM, Miron A, Garber J, Wang M, Componeschi K, Boghossian L, Miron PL, Nathanson KL, Tung N.

Fam Cancer. 2011 Jun;10(2):225-31. doi: 10.1007/s10689-011-9426-1.

PubMed [citation]

PMID:: 21365267
PMCID:: PMC3836668

See all PubMed Citations (22)

Details of each submission

From Ambry Genetics, SCV000185544.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (16)

Description

The c.509_510delGA pathogenic mutation, located in coding exon 4 of the PALB2 gene, results from a deletion of two nucleotides at nucleotide positions 509 to 510, causing a translational frameshift with a predicted alternate stop codon (p.R170Ifs*14). This alteration has been reported in familial breast, ovarian, and pancreatic cancer cohorts with carrier ethnicity data supporting c.509_510delGA as a founder mutation of central European origin (Dansonka-Mieszkowska A et al. BMC Med. Genet. 2010 Feb;11:20; Slater EP et al. Clin. Genet. 2010 Nov;78:490-4; Casadei S et al. Cancer Res. 2011 Mar;71:2222-9; Noskowicz M et al. Fam. Cancer. 2014 Jun;13:137-42; Cybulski C et al. Clin. Genet. 2015 Oct;88:366-70; Desmond A et al. JAMA Oncol. 2015 Oct;1:943-51; Kluska A et al. BMC Med. Genomics. 2017 Mar;10:14). Additional data has led authors to suggest that this is one of two PALB2 founder mutations associated with poor outcome in Polish breast cancer patients (Cybulski C et al. Lancet Oncol. 2015 Jun;16:638-44). Further, a functional characterization of this alteration showed that the truncated protein results in weakly bound DNA substrates, suggesting that the loss of the second DNA binding domain affects the affinity for DNA, resulting in significantly impaired DNA binding (Pauty J et al. Nucleic Acids Res. 2017 Mar;45:2644-2657). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From University of Washington Department of Laboratory Medicine, University of Washington, SCV000266111.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

From Color Diagnostics, LLC DBA Color Health, SCV000686065.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (13)

Description

This variant deletes 2 nucleotides in exon 4 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. A functional study reported that this variant impacts PALB2 binding to DNA (PMID: 28158555). This variant has been detected in over 40 individuals affected with breast, ovarian and pancreatic cancer (PMID: 20122277, 20412113, 20582465, 21285249, 24136930, 24061862, 25099575, 25186627, 26270727, 27106063, 33471991; Leiden Open Variation Database DB-ID PALB2_010036). This variant has been identified in 9/251446 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneKor MSA, SCV000821754.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This mutation is a 2 bp deletion at codon 509 of the PALB2 gene. It results in a frame-shift creating new stop codon 14 amino acid residues later, thus resulting in absent or disrupted protein product. Truncating variants in PALB2 are known to be pathogenic. This particular truncation has been reported in the literature in association with familial breast and pancreatic cancers (PMID: 20412113; PMID: 21285249). The mutation database ClinVar contains multiple entries for this variant (Variation ID: 126757).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mendelics, SCV000839054.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C., SCV002819235.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

ClinVar

Relating variation to medicine