NM_024675.4(PALB2):c.3026del (p.Pro1009fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jul 3, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000133484.4

Allele description [Variation Report for NM_024675.4(PALB2):c.3026del (p.Pro1009fs)]

NM_024675.4(PALB2):c.3026del (p.Pro1009fs)

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.3026del (p.Pro1009fs)

HGVS:

NC_000016.10:g.23621453del
NG_007406.1:g.24909del
NM_024675.4:c.3026delMANE SELECT
NP_078951.2:p.Pro1009fs
NP_078951.2:p.Pro1009fs
LRG_308t1:c.3026del
LRG_308:g.24909del
LRG_308p1:p.Pro1009fs
NC_000016.9:g.23632770del
NC_000016.9:g.23632774del
NM_024675.3:c.3026del
NM_024675.3:c.3026delC
p.P1009LfsX6

Protein change:

P1009fs

Links:

dbSNP: rs180177131

NCBI 1000 Genomes Browser:

rs180177131

Molecular consequence:

NM_024675.4:c.3026del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000188558	SNPedia	no assertion criteria provided	pathogenic	germline	not provided	PubMed (1) [See all records that cite this PMID]
SCV000211481	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jul 3, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000188558

SNPedia

no assertion criteria provided

pathogenic

germline

not provided

PubMed (1)
[See all records that cite this PMID]

SCV000211481

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jul 3, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Breast-cancer risk in families with mutations in PALB2.

Antoniou AC, Casadei S, Heikkinen T, Barrowdale D, Pylkäs K, Roberts J, Lee A, Subramanian D, De Leeneer K, Fostira F, Tomiak E, Neuhausen SL, Teo ZL, Khan S, Aittomäki K, Moilanen JS, Turnbull C, Seal S, Mannermaa A, Kallioniemi A, Lindeman GJ, Buys SS, et al.

N Engl J Med. 2014 Aug 7;371(6):497-506. doi: 10.1056/NEJMoa1400382.

PubMed [citation]

PMID:: 25099575
PMCID:: PMC4157599

Details of each submission

From SNPedia, SCV000188558.1

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

Description

Converted during submission to Pathogenic.

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

From GeneDx, SCV000211481.7

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

Description

This deletion of one nucleotide is denoted PALB2 c.3026delC at the cDNA level and p.Pro1009LeufsX6 (P1009LfsX6) at the protein level. The normal sequence, with the base that is deleted in braces, is GCCCC[C]TGAG. The deletion causes a frameshift, which changes a Proline to a Leucine at codon 1009, and creates a premature stop codon at position 6 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. PALB2 3026delC, previously denoted as 3022delC, has been reported in at least three individuals with breast cancer (Casadei 2011, Susswein 2015). We consider this variant to be pathogenic.

#	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

Last Updated: Sep 8, 2024

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