NM_024675.4(PALB2):c.484T>G (p.Cys162Gly) AND Familial cancer of breast

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 3, 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:: RCV003608360.2

Allele description [Variation Report for NM_024675.4(PALB2):c.484T>G (p.Cys162Gly)]

NM_024675.4(PALB2):c.484T>G (p.Cys162Gly)

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.484T>G (p.Cys162Gly)

HGVS:

NC_000016.10:g.23636062A>C
NG_007406.1:g.10296T>G
NM_001407296.1:c.424T>G
NM_001407297.1:c.484T>G
NM_001407298.1:c.484T>G
NM_001407299.1:c.484T>G
NM_001407300.1:c.484T>G
NM_001407301.1:c.484T>G
NM_001407302.1:c.484T>G
NM_001407304.1:c.-402T>G
NM_001407305.1:c.-402T>G
NM_001407306.1:c.-402T>G
NM_001407307.1:c.-402T>G
NM_001407308.1:c.-402T>G
NM_001407309.1:c.-402T>G
NM_001407310.1:c.-402T>G
NM_001407311.1:c.-402T>G
NM_001407312.1:c.-105+5048T>G
NM_001407313.1:c.-105+5048T>G
NM_001407314.1:c.48+5048T>G
NM_024675.4:c.484T>GMANE SELECT
NP_001394225.1:p.Cys142Gly
NP_001394226.1:p.Cys162Gly
NP_001394227.1:p.Cys162Gly
NP_001394228.1:p.Cys162Gly
NP_001394229.1:p.Cys162Gly
NP_001394230.1:p.Cys162Gly
NP_001394231.1:p.Cys162Gly
NP_078951.2:p.Cys162Gly
NP_078951.2:p.Cys162Gly
LRG_308t1:c.484T>G
LRG_308:g.10296T>G
LRG_308p1:p.Cys162Gly
NC_000016.9:g.23647383A>C
NM_024675.3:c.484T>G

Protein change:

C142G

Molecular consequence:

NM_001407304.1:c.-402T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407305.1:c.-402T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407306.1:c.-402T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407307.1:c.-402T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407308.1:c.-402T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407309.1:c.-402T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407310.1:c.-402T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407311.1:c.-402T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407312.1:c.-105+5048T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407313.1:c.-105+5048T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407314.1:c.48+5048T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407296.1:c.424T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407297.1:c.484T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407298.1:c.484T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407299.1:c.484T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407300.1:c.484T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407301.1:c.484T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407302.1:c.484T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_024675.4:c.484T>G - 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

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Burkholderia cenocepacia strain VC2307 chromosome 1, complete sequence
Burkholderia cenocepacia strain VC2307 chromosome 1, complete sequence
gi|1149334058|ref|NZ_CP019666.1|

Nucleotide
pocC4W8
pocC4W8

biosample
pocC4W3
pocC4W3

biosample
synphilin-1 isoform X1 [Rhinatrema bivittatum]
synphilin-1 isoform X1 [Rhinatrema bivittatum]
gi|1694538845|ref|XP_029475853.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004457564	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 3, 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

SCV004457564

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 3, 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, SCV004457564.1

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

Description

This variant has not been reported in the literature in individuals affected with PALB2-related conditions. This sequence change replaces cysteine, which is neutral and slightly polar, with glycine, which is neutral and non-polar, at codon 162 of the PALB2 protein (p.Cys162Gly). This variant is not present in population databases (gnomAD no frequency). 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 glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#	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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