NM_024675.4(PALB2):c.409G>A (p.Gly137Ser) AND Familial cancer of breast

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 16, 2023
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:: RCV000803385.8

Allele description [Variation Report for NM_024675.4(PALB2):c.409G>A (p.Gly137Ser)]

NM_024675.4(PALB2):c.409G>A (p.Gly137Ser)

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.409G>A (p.Gly137Ser)

HGVS:

NC_000016.10:g.23636137C>T
NG_007406.1:g.10221G>A
NM_024675.4:c.409G>AMANE SELECT
NP_078951.2:p.Gly137Ser
NP_078951.2:p.Gly137Ser
LRG_308t1:c.409G>A
LRG_308:g.10221G>A
LRG_308p1:p.Gly137Ser
NC_000016.9:g.23647458C>T
NM_024675.3:c.409G>A

Protein change:

G137S

Links:

dbSNP: rs1397816581

NCBI 1000 Genomes Browser:

rs1397816581

Molecular consequence:

NM_024675.4:c.409G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial cancer of breast
Synonyms:: Breast cancer, familial; Hereditary breast cancer
Identifiers:: MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480

Recent activity

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JGI_XZT9939.rev NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587856 3',...
JGI_XZT9939.rev NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587856 3', mRNA sequence
gi|57045292|gnl|dbEST|26936429|gb|C 65.1|

Nucleotide
JGI_XZT9708.rev NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587893 3',...
JGI_XZT9708.rev NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587893 3', mRNA sequence
gi|57044466|gnl|dbEST|26936084|gb|C 20.1|

Nucleotide
dai40d11.x1 NICHD_XGC_Sp1 Xenopus laevis cDNA clone IMAGE:4964037 3', mRNA seque...
dai40d11.x1 NICHD_XGC_Sp1 Xenopus laevis cDNA clone IMAGE:4964037 3', mRNA sequence
gi|15266512|gnl|dbEST|9284391|gb|BI 5.1|

Nucleotide
cm17h06.w1 Blackshear/Soares normalized Xenopus egg library Xenopus laevis cDNA ...
cm17h06.w1 Blackshear/Soares normalized Xenopus egg library Xenopus laevis cDNA clone PBX0116H06 5', mRNA sequence
gi|7399658|gnl|dbEST|4078887|gb|AW6 .1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000943254	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 16, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000943254

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 16, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000943254.4

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 137 of the PALB2 protein (p.Gly137Ser). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 628639). This variant has not been reported in the literature in individuals affected with PALB2-related conditions. This variant is not present in population databases (gnomAD no frequency).

#	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: Sep 29, 2024

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