NM_024675.4(PALB2):c.3074C>A (p.Ala1025Asp) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 12, 2021
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:: RCV003585681.1

Allele description [Variation Report for NM_024675.4(PALB2):c.3074C>A (p.Ala1025Asp)]

NM_024675.4(PALB2):c.3074C>A (p.Ala1025Asp)

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.3074C>A (p.Ala1025Asp)

HGVS:

NC_000016.10:g.23621401G>T
NG_007406.1:g.24957C>A
NM_001407296.1:c.3014C>A
NM_001407297.1:c.3002C>A
NM_001407298.1:c.2912C>A
NM_001407299.1:c.3074C>A
NM_001407300.1:c.2834+2608C>A
NM_001407301.1:c.3074C>A
NM_001407302.1:c.2912C>A
NM_001407304.1:c.2189C>A
NM_001407305.1:c.2189C>A
NM_001407306.1:c.2189C>A
NM_001407307.1:c.2027C>A
NM_001407308.1:c.2189C>A
NM_001407309.1:c.2189C>A
NM_001407310.1:c.2189C>A
NM_001407311.1:c.2189C>A
NM_001407312.1:c.1286C>A
NM_001407313.1:c.1286C>A
NM_001407314.1:c.608C>A
NM_024675.4:c.3074C>AMANE SELECT
NP_001394225.1:p.Ala1005Asp
NP_001394226.1:p.Ala1001Asp
NP_001394227.1:p.Ala971Asp
NP_001394228.1:p.Ala1025Asp
NP_001394230.1:p.Ala1025Asp
NP_001394231.1:p.Ala971Asp
NP_001394233.1:p.Ala730Asp
NP_001394234.1:p.Ala730Asp
NP_001394235.1:p.Ala730Asp
NP_001394236.1:p.Ala676Asp
NP_001394237.1:p.Ala730Asp
NP_001394238.1:p.Ala730Asp
NP_001394239.1:p.Ala730Asp
NP_001394240.1:p.Ala730Asp
NP_001394241.1:p.Ala429Asp
NP_001394242.1:p.Ala429Asp
NP_001394243.1:p.Ala203Asp
NP_078951.2:p.Ala1025Asp
NP_078951.2:p.Ala1025Asp
LRG_308t1:c.3074C>A
LRG_308:g.24957C>A
LRG_308p1:p.Ala1025Asp
NC_000016.9:g.23632722G>T
NM_024675.3:c.3074C>A

Protein change:

A1001D

Molecular consequence:

NM_001407300.1:c.2834+2608C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407296.1:c.3014C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407297.1:c.3002C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407298.1:c.2912C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407299.1:c.3074C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407301.1:c.3074C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407302.1:c.2912C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407304.1:c.2189C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407305.1:c.2189C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407306.1:c.2189C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407307.1:c.2027C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407308.1:c.2189C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407309.1:c.2189C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407310.1:c.2189C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407311.1:c.2189C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407312.1:c.1286C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407313.1:c.1286C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407314.1:c.608C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024675.4:c.3074C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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PREDICTED: Pteropus alecto calpain 3 (CAPN3), transcript variant X2, mRNA
PREDICTED: Pteropus alecto calpain 3 (CAPN3), transcript variant X2, mRNA
gi|1387533606|ref|XM_006920455.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004357822	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 12, 2021)	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

SCV004357822

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 12, 2021)

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

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 Color Diagnostics, LLC DBA Color Health, SCV004357822.1

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

Description

This missense variant replaces alanine with aspartic acid at codon 1025 of the PALB2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is 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: Feb 20, 2024

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