NM_024675.4(PALB2):c.1470C>T (p.Pro490=) AND not specified

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Aug 15, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000212795.11

Allele description [Variation Report for NM_024675.4(PALB2):c.1470C>T (p.Pro490=)]

NM_024675.4(PALB2):c.1470C>T (p.Pro490=)

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.1470C>T (p.Pro490=)

Other names:

p.P490P:CCC>CCT

HGVS:

NC_000016.10:g.23635076G>A
NG_007406.1:g.11282C>T
NM_024675.4:c.1470C>TMANE SELECT
NP_078951.2:p.Pro490=
NP_078951.2:p.Pro490=
LRG_308t1:c.1470C>T
LRG_308:g.11282C>T
LRG_308p1:p.Pro490=
NC_000016.9:g.23646397G>A
NM_024675.3:c.1470C>T
p.P490P
p.Pro490Pro

Links:

dbSNP: rs45612837

NCBI 1000 Genomes Browser:

rs45612837

Molecular consequence:

NM_024675.4:c.1470C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000170871	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (Feb 28, 2014)	germline	clinical testing	Citation Link,
SCV000889572	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Benign (Jan 3, 2020)	unknown	clinical testing	PubMed (9) [See all records that cite these PMIDs] 17200668, 24206657, 20582465, 26283626, 26564480, 25225577, 21165770, 23448497, 26467025
SCV002066590	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Sep 24, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002760834	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Aug 15, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene.

Rahman N, Seal S, Thompson D, Kelly P, Renwick A, Elliott A, Reid S, Spanova K, Barfoot R, Chagtai T, Jayatilake H, McGuffog L, Hanks S, Evans DG, Eccles D; Breast Cancer Susceptibility Collaboration (UK)., Easton DF, Stratton MR.

Nat Genet. 2007 Feb;39(2):165-7. Epub 2006 Dec 31.

PubMed [citation]

PMID:: 17200668
PMCID:: PMC2871593

Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2.

Nguyen-Dumont T, Teo ZL, Pope BJ, Hammet F, Mahmoodi M, Tsimiklis H, Sabbaghian N, Tischkowitz M, Foulkes WD; Kathleen Cuningham Foundation Consortium for research into Familial Breast cancer (kConFab)., Giles GG, Hopper JL; Australian Breast Cancer Family Registry., Southey MC, Park DJ.

BMC Med Genomics. 2013 Nov 8;6:48. doi: 10.1186/1755-8794-6-48.

PubMed [citation]

PMID:: 24206657
PMCID:: PMC3829211

See all PubMed Citations (10)

Details of each submission

From GeneDx, SCV000170871.11

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#	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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000889572.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

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

From Genetic Services Laboratory, University of Chicago, SCV002066590.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV002760834.3

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

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

Last Updated: Oct 20, 2024

ClinVar

Relating variation to medicine