NM_024675.4(PALB2):c.1492G>T (p.Asp498Tyr) AND not provided

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Jun 16, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000858743.17

Allele description [Variation Report for NM_024675.4(PALB2):c.1492G>T (p.Asp498Tyr)]

NM_024675.4(PALB2):c.1492G>T (p.Asp498Tyr)

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.1492G>T (p.Asp498Tyr)

Other names:

p.D498Y:GAC>TAC

HGVS:

NC_000016.10:g.23635054C>A
NG_007406.1:g.11304G>T
NM_024675.4:c.1492G>TMANE SELECT
NP_078951.2:p.Asp498Tyr
NP_078951.2:p.Asp498Tyr
LRG_308t1:c.1492G>T
LRG_308:g.11304G>T
LRG_308p1:p.Asp498Tyr
NC_000016.9:g.23646375C>A
NM_024675.3:c.1492G>T
p.D498Y

Protein change:

D498Y

Links:

dbSNP: rs75023630

NCBI 1000 Genomes Browser:

rs75023630

Molecular consequence:

NM_024675.4:c.1492G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000211557	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Jun 16, 2021)	germline	clinical testing	Citation Link,
SCV000601730	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (Mar 20, 2019)	germline	clinical testing	PubMed (10) [See all records that cite these PMIDs] 26692951, 25186627, 23977390, 26411315, 26283626, 27783279, 28767289, 28580595, 28825143, 26467025
SCV001193114	Leiden Open Variation Database	no assertion criteria provided	Likely benign (May 13, 2019)	germline	curation	PubMed (3) [See all records that cite these PMIDs] 23977390, 25186627, 30287823

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000211557

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Jun 16, 2021)

germline

clinical testing

Citation Link,

SCV000601730

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely benign
(Mar 20, 2019)

germline

clinical testing

PubMed (10)
[See all records that cite these PMIDs]

SCV001193114

Leiden Open Variation Database

no assertion criteria provided

Likely benign
(May 13, 2019)

germline

curation

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	curation
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Targeted next-generation sequencing of cancer genes identified frequent TP53 and ATRX mutations in leiomyosarcoma.

Yang CY, Liau JY, Huang WJ, Chang YT, Chang MC, Lee JC, Tsai JH, Su YN, Hung CC, Jeng YM.

Am J Transl Res. 2015;7(10):2072-81.

PubMed [citation]

PMID:: 26692951
PMCID:: PMC4656784

Analysis of PALB2 mutations in 155 Japanese patients with breast and/or ovarian cancer.

Nakagomi H, Sakamoto I, Hirotsu Y, Amemiya K, Mochiduki H, Omata M.

Int J Clin Oncol. 2016 Apr;21(2):270-275. doi: 10.1007/s10147-015-0906-4. Epub 2015 Sep 28.

PubMed [citation]

PMID:: 26411315

See all PubMed Citations (11)

Details of each submission

From GeneDx, SCV000211557.9

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

Description

This variant is associated with the following publications: (PMID: 26411315, 28580595, 23977390, 25186627, 26283626, 26692951, 23555315, 27783279, 28796317, 28825143, 30309218, 28767289, 29338689, 31757951)

#	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		not provided	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000601730.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (10)

#	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

From Leiden Open Variation Database, SCV001193114.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (3)

Description

Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitters to LOVD: Marc Tischkowitz, Melissa DeRycke, Yukihide Momozawa.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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