NM_024675.4(PALB2):c.2677G>T (p.Asp893Tyr) AND Breast-ovarian cancer, familial, susceptibility to, 5

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 3, 2024
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:: RCV003991027.1

Allele description [Variation Report for NM_024675.4(PALB2):c.2677G>T (p.Asp893Tyr)]

NM_024675.4(PALB2):c.2677G>T (p.Asp893Tyr)

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.2677G>T (p.Asp893Tyr)

HGVS:

NC_000016.10:g.23626307C>A
NG_007406.1:g.20051G>T
NM_024675.4:c.2677G>TMANE SELECT
NP_078951.2:p.Asp893Tyr
NP_078951.2:p.Asp893Tyr
LRG_308t1:c.2677G>T
LRG_308:g.20051G>T
LRG_308p1:p.Asp893Tyr
NC_000016.9:g.23637628C>A
NM_024675.3:c.2677G>T

Protein change:

D893Y

Links:

dbSNP: rs765077104

NCBI 1000 Genomes Browser:

rs765077104

Molecular consequence:

NM_024675.4:c.2677G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Breast-ovarian cancer, familial, susceptibility to, 5 (BROVCA5)
Identifiers:: MONDO: MONDO:0957530; MedGen: C5830615; OMIM: 620442

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004808368	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 3, 2024)	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

SCV004808368

KCCC/NGS Laboratory, Kuwait Cancer Control Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 3, 2024)

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	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004808368.1

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 893 of the PALB2 protein (p.Asp893Tyr). This variant is present in population databases (rs765077104, gnomAD 0.006%). 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: 410135). Computational prediction suggests that this variant may not impact protein structure and function. Functional studies have not been reported for this variant.. 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	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine