NM_024675.4(PALB2):c.1695T>A (p.Ser565Arg) AND Familial cancer of breast

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 1, 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:: RCV003500773.2

Allele description [Variation Report for NM_024675.4(PALB2):c.1695T>A (p.Ser565Arg)]

NM_024675.4(PALB2):c.1695T>A (p.Ser565Arg)

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.1695T>A (p.Ser565Arg)

HGVS:

NC_000016.10:g.23630459A>T
NG_007406.1:g.15899T>A
NM_001407296.1:c.1635T>A
NM_001407297.1:c.1695T>A
NM_001407298.1:c.1695T>A
NM_001407299.1:c.1695T>A
NM_001407300.1:c.1695T>A
NM_001407301.1:c.1695T>A
NM_001407302.1:c.1695T>A
NM_001407304.1:c.810T>A
NM_001407305.1:c.810T>A
NM_001407306.1:c.810T>A
NM_001407307.1:c.810T>A
NM_001407308.1:c.810T>A
NM_001407309.1:c.810T>A
NM_001407310.1:c.810T>A
NM_001407311.1:c.810T>A
NM_001407312.1:c.-94T>A
NM_001407313.1:c.-94T>A
NM_024675.4:c.1695T>AMANE SELECT
NP_001394225.1:p.Ser545Arg
NP_001394226.1:p.Ser565Arg
NP_001394227.1:p.Ser565Arg
NP_001394228.1:p.Ser565Arg
NP_001394229.1:p.Ser565Arg
NP_001394230.1:p.Ser565Arg
NP_001394231.1:p.Ser565Arg
NP_001394233.1:p.Ser270Arg
NP_001394234.1:p.Ser270Arg
NP_001394235.1:p.Ser270Arg
NP_001394236.1:p.Ser270Arg
NP_001394237.1:p.Ser270Arg
NP_001394238.1:p.Ser270Arg
NP_001394239.1:p.Ser270Arg
NP_001394240.1:p.Ser270Arg
NP_078951.2:p.Ser565Arg
NP_078951.2:p.Ser565Arg
LRG_308t1:c.1695T>A
LRG_308:g.15899T>A
LRG_308p1:p.Ser565Arg
NC_000016.9:g.23641780A>T
NM_024675.3:c.1695T>A

Protein change:

S270R

Molecular consequence:

NM_001407296.1:c.1635T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407297.1:c.1695T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407298.1:c.1695T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407299.1:c.1695T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407300.1:c.1695T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407301.1:c.1695T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407302.1:c.1695T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407304.1:c.810T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407305.1:c.810T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407306.1:c.810T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407307.1:c.810T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407308.1:c.810T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407309.1:c.810T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407310.1:c.810T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407311.1:c.810T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024675.4:c.1695T>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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ABC-type organic anion transporter ABCA8 isoform 3 [Homo sapiens]
ABC-type organic anion transporter ABCA8 isoform 3 [Homo sapiens]
gi|572882683|ref|NP_001275915.1|

Protein
Homo sapiens tetraspanin 6 (TSPAN6), transcript variant 5, mRNA
Homo sapiens tetraspanin 6 (TSPAN6), transcript variant 5, mRNA
gi|523567560|ref|NM_001278743.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004253092	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 1, 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

SCV004253092

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 1, 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, SCV004253092.1

#	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 serine, which is neutral and polar, with arginine, which is basic and polar, at codon 565 of the PALB2 protein (p.Ser565Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PALB2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1778225). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PALB2 protein function with a negative predictive value of 80%. 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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