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NM_024675.4(PALB2):c.2100_2110del (p.Ser701fs) AND Hereditary breast ovarian cancer syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 7, 2021
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:
RCV001775143.4

Allele description [Variation Report for NM_024675.4(PALB2):c.2100_2110del (p.Ser701fs)]

NM_024675.4(PALB2):c.2100_2110del (p.Ser701fs)

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.2100_2110del (p.Ser701fs)
HGVS:
  • NC_000016.10:g.23630045_23630055del
  • NG_007406.1:g.16304_16314del
  • NM_024675.3:c.2100_2110del11
  • NM_024675.4:c.2100_2110delMANE SELECT
  • NP_078951.2:p.Ser701fs
  • LRG_308t1:c.2100_2110del
  • LRG_308:g.16304_16314del
  • NC_000016.9:g.23641365_23641375del
  • NC_000016.9:g.23641366_23641376del
  • NM_024675.3:c.2100_2110del
  • NM_024675.3:c.2100_2110del11
  • NM_024675.3:c.2100_2110delATCCATATTAC
Protein change:
S701fs
Links:
dbSNP: rs1555460490
NCBI 1000 Genomes Browser:
rs1555460490
Molecular consequence:
  • NM_024675.4:c.2100_2110del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Hereditary breast ovarian cancer syndrome
Synonyms:
Hereditary breast and ovarian cancer syndrome; Hereditary breast and ovarian cancer; Hereditary breast and ovarian cancer syndrome (HBOC); See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0003582; MeSH: D061325; MedGen: C0677776; Orphanet: 145

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002012417St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Pathogenic
(Oct 7, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV002012417.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The PALB2 c.2100_2110del (p.Ser701LeufsTer10) change deletes 11 nucleotides in exon 5 of the PALB2 gene to cause a frameshift and the creation of a premature stop codon. This change is predicted to cause protein truncation or absence of the protein due to nonsense-mediated decay (PVS1). This variant is absent in gnomAD v2.1.1 (PM2_supporting; https://gnomad.broadinstitute.org/) and is not reported in a database of women older than 70 years of age who have never had cancer (FLOSSIES database, https://whi.color.com/). To our knowledge, this variant has not been reported in individuals affected with hereditary breast and ovarian cancer or Fanconi anemia. However, other truncating variants in exon 5 have been reported in individuals with breast and/or ovarian cancer and are known to be pathogenic (PM5_supporting). In summary, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP criteria: PVS1, PM2_supporting, PM5_supporting.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024