NM_024675.4(PALB2):c.2060del (p.Pro687fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 16, 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:: RCV004517747.1

Allele description [Variation Report for NM_024675.4(PALB2):c.2060del (p.Pro687fs)]

NM_024675.4(PALB2):c.2060del (p.Pro687fs)

Gene:

PALB2:partner and localizer of BRCA2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p12.2

Genomic location:

Preferred name:

NM_024675.4(PALB2):c.2060del (p.Pro687fs)

HGVS:

NC_000016.10:g.23630095del
NG_007406.1:g.16264del
NM_001407296.1:c.2000del
NM_001407297.1:c.2060del
NM_001407298.1:c.2060del
NM_001407299.1:c.2060del
NM_001407300.1:c.2060del
NM_001407301.1:c.2060del
NM_001407302.1:c.2060del
NM_001407304.1:c.1175del
NM_001407305.1:c.1175del
NM_001407306.1:c.1175del
NM_001407307.1:c.1175del
NM_001407308.1:c.1175del
NM_001407309.1:c.1175del
NM_001407310.1:c.1175del
NM_001407311.1:c.1175del
NM_001407312.1:c.272del
NM_001407313.1:c.272del
NM_001407314.1:c.49-819del
NM_024675.4:c.2060delMANE SELECT
NP_001394225.1:p.Pro667fs
NP_001394226.1:p.Pro687fs
NP_001394227.1:p.Pro687fs
NP_001394228.1:p.Pro687fs
NP_001394229.1:p.Pro687fs
NP_001394230.1:p.Pro687fs
NP_001394231.1:p.Pro687fs
NP_001394233.1:p.Pro392fs
NP_001394234.1:p.Pro392fs
NP_001394235.1:p.Pro392fs
NP_001394236.1:p.Pro392fs
NP_001394237.1:p.Pro392fs
NP_001394238.1:p.Pro392fs
NP_001394239.1:p.Pro392fs
NP_001394240.1:p.Pro392fs
NP_001394241.1:p.Pro91fs
NP_001394242.1:p.Pro91fs
NP_078951.2:p.Pro687Glnfs
NP_078951.2:p.Pro687fs
LRG_308t1:c.2059del
LRG_308:g.16264del
LRG_308p1:p.Pro687Glnfs
NC_000016.9:g.23641416del
NM_024675.3:c.2059delC
NM_024675.3:c.2060delC

Protein change:

P392fs

Molecular consequence:

NM_001407296.1:c.2000del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407297.1:c.2060del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407298.1:c.2060del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407299.1:c.2060del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407300.1:c.2060del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407301.1:c.2060del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407302.1:c.2060del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407304.1:c.1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407305.1:c.1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407306.1:c.1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407307.1:c.1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407308.1:c.1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407309.1:c.1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407310.1:c.1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407311.1:c.1175del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407312.1:c.272del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407313.1:c.272del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024675.4:c.2060del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407314.1:c.49-819del - intron variant - [Sequence Ontology: SO:0001627]

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

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005028907	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Nov 16, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005028907

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Nov 16, 2023)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV005028907.1

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

Description

The c.2060delC pathogenic mutation, located in coding exon 5 of the PALB2 gene, results from a deletion of one nucleotide at nucleotide position 2060, causing a translational frameshift with a predicted alternate stop codon (p.P687Qfs*22). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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: May 7, 2024

ClinVar

Relating variation to medicine