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NM_024675.4(PALB2):c.3116A>C (p.Asn1039Thr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 1, 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:
RCV000523781.1

Allele description [Variation Report for NM_024675.4(PALB2):c.3116A>C (p.Asn1039Thr)]

NM_024675.4(PALB2):c.3116A>C (p.Asn1039Thr)

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.3116A>C (p.Asn1039Thr)
HGVS:
  • NC_000016.10:g.23614089T>G
  • NG_007406.1:g.32269A>C
  • NM_024675.4:c.3116A>CMANE SELECT
  • NP_078951.2:p.Asn1039Thr
  • NP_078951.2:p.Asn1039Thr
  • LRG_308t1:c.3116A>C
  • LRG_308:g.32269A>C
  • LRG_308p1:p.Asn1039Thr
  • NC_000016.9:g.23625410T>G
  • NM_024675.3:c.3116A>C
Protein change:
N1039T
Links:
dbSNP: rs1555458829
NCBI 1000 Genomes Browser:
rs1555458829
Molecular consequence:
  • NM_024675.4:c.3116A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000618308GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Mar 1, 2017) 		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, SCV000618308.2

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

Description

This variant is denoted PALB2 c.3116A>C at the cDNA level, p.Asn1039Thr (N1039T) at the protein level, and results in the change of an Asparagine to a Threonine (AAT>ACT). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. PALB2 Asn1039Thr was not observed in large population cohorts (Lek 2016, The 1000 Genomes Consortium 2015, NHLBI Exome Sequencing Project). Since Asparagine and Threonine share similar properties, this is considered a conservative amino acid substitution. PALB2 Asn1039Thr occurs at a position that is conserved in mammals and is located in the WD4 repeat, the region of interaction with POLH, RAD51,and BRCA2, and the region required for POLH DNA synthesis stimulation (UniProt). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available evidence, it is unclear whether PALB2 Asn1039Thr 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: Sep 29, 2024