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NM_024675.4(PALB2):c.10C>T (p.Pro4Ser) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 9, 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:
RCV000212763.4

Allele description [Variation Report for NM_024675.4(PALB2):c.10C>T (p.Pro4Ser)]

NM_024675.4(PALB2):c.10C>T (p.Pro4Ser)

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.10C>T (p.Pro4Ser)
Other names:
p.P4S:CCT>TCT
HGVS:
  • NC_000016.10:g.23641148G>A
  • NG_007406.1:g.5210C>T
  • NM_024675.4:c.10C>TMANE SELECT
  • NP_078951.2:p.Pro4Ser
  • NP_078951.2:p.Pro4Ser
  • LRG_308t1:c.10C>T
  • LRG_308:g.5210C>T
  • LRG_308p1:p.Pro4Ser
  • NC_000016.9:g.23652469G>A
  • NM_024675.3:c.10C>T
  • p.P4S
Protein change:
P4S
Links:
dbSNP: rs587782483
NCBI 1000 Genomes Browser:
rs587782483
Molecular consequence:
  • NM_024675.4:c.10C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000211559GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Uncertain significance
(Apr 9, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000211559.11

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

Description

This variant is denoted PALB2 c.10C>T at the cDNA level, p.Pro4Ser (P4S) at the protein level, and results in the change of a Proline to a Serine (CCT>TCT). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. PALB2 Pro4Ser 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 Proline and Serine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. PALB2 Pro4Ser occurs at a position that is not conserved and is located in the regions of interaction with BRCA1 and RAD51, the DNA-binding region, and the region required for oligomerization and focal concentration at DNA damage sites (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 Pro4Ser is pathogenic or benign. 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: Sep 29, 2024