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NM_024675.4(PALB2):c.1552T>C (p.Ser518Pro) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 29, 2016
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:
RCV000236344.1

Allele description [Variation Report for NM_024675.4(PALB2):c.1552T>C (p.Ser518Pro)]

NM_024675.4(PALB2):c.1552T>C (p.Ser518Pro)

Gene:
PALB2:partner and localizer of BRCA2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p12.2
Genomic location:
Preferred name:
NM_024675.4(PALB2):c.1552T>C (p.Ser518Pro)
HGVS:
  • NC_000016.10:g.23634994A>G
  • NG_007406.1:g.11364T>C
  • NM_024675.4:c.1552T>CMANE SELECT
  • NP_078951.2:p.Ser518Pro
  • NP_078951.2:p.Ser518Pro
  • LRG_308t1:c.1552T>C
  • LRG_308:g.11364T>C
  • LRG_308p1:p.Ser518Pro
  • NC_000016.9:g.23646315A>G
  • NM_024675.3:c.1552T>C
  • p.S518P
Protein change:
S518P
Links:
dbSNP: rs587782735
NCBI 1000 Genomes Browser:
rs587782735
Molecular consequence:
  • NM_024675.4:c.1552T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000293898GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Feb 29, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000293898.9

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

Description

This variant is denoted PALB2 c.1552T>C at the cDNA level, p.Ser518Pro (S518P) at the protein level, and results in the change of a Serine to a Proline (TCA>CCA). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. PALB2 Ser518Pro was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Serine and Proline differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. PALB2 Ser518Pro occurs at a position that is not conserved and is located in the DNA binding region (UniProt). In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Based on currently available evidence, it is unclear whether PALB2 Ser518Pro is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.

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

Last Updated: Dec 24, 2023