NM_024675.4(PALB2):c.493G>A (p.Gly165Ser) AND Familial cancer of breast

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 29, 2019
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:: RCV001204264.9

Allele description [Variation Report for NM_024675.4(PALB2):c.493G>A (p.Gly165Ser)]

NM_024675.4(PALB2):c.493G>A (p.Gly165Ser)

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.493G>A (p.Gly165Ser)

HGVS:

NC_000016.10:g.23636053C>T
NG_007406.1:g.10305G>A
NM_024675.4:c.493G>AMANE SELECT
NP_078951.2:p.Gly165Ser
LRG_308t1:c.493G>A
LRG_308:g.10305G>A
NC_000016.9:g.23647374C>T
NM_024675.3:c.493G>A

Protein change:

G165S

Links:

dbSNP: rs1967043594

NCBI 1000 Genomes Browser:

rs1967043594

Molecular consequence:

NM_024675.4:c.493G>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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PREDICTED: Homo sapiens ArfGAP with coiled-coil, ankyrin repeat and PH domains 3...
PREDICTED: Homo sapiens ArfGAP with coiled-coil, ankyrin repeat and PH domains 3 (ACAP3), transcript variant X4, mRNA
gi|2217263718|ref|XM_011540608.3|

Nucleotide
mucin-19 isoform X7 [Anopheles gambiae]
mucin-19 isoform X7 [Anopheles gambiae]
gi|2637394821|ref|XP_061503321.1|

Protein
protein winged eye isoform X4 [Anopheles gambiae]
protein winged eye isoform X4 [Anopheles gambiae]
gi|2637394809|ref|XP_061503314.1|

Protein
Fusobacterium sp. HMSC073F01, whole genome shotgun sequencing project
Fusobacterium sp. HMSC073F01, whole genome shotgun sequencing project
gi|1080408224|gb|LTHT00000000.1|LTH 0000

Nucleotide
SRX3503144 (1)
SRA

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001375463	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 29, 2019)	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

SCV001375463

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 29, 2019)

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, SCV001375463.5

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

Description

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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with PALB2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with serine at codon 165 of the PALB2 protein (p.Gly165Ser). The glycine residue is weakly conserved and there is a small physicochemical difference between glycine and serine.

#	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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