NM_024675.4(PALB2):c.3037_3040delinsGTG (p.Ile1013fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 19, 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:: RCV003311311.2

Allele description [Variation Report for NM_024675.4(PALB2):c.3037_3040delinsGTG (p.Ile1013fs)]

NM_024675.4(PALB2):c.3037_3040delinsGTG (p.Ile1013fs)

Gene:

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

Variant type:

Indel

Cytogenetic location:

16p12.2

Genomic location:

Preferred name:

NM_024675.4(PALB2):c.3037_3040delinsGTG (p.Ile1013fs)

HGVS:

NC_000016.10:g.23621435_23621438delinsCAC
NG_007406.1:g.24920_24923delinsGTG
NM_001407296.1:c.2977_2980delinsGTG
NM_001407297.1:c.2965_2968delinsGTG
NM_001407298.1:c.2875_2878delinsGTG
NM_001407299.1:c.3037_3040delinsGTG
NM_001407300.1:c.2834+2571_2834+2574delinsGTG
NM_001407301.1:c.3037_3040delinsGTG
NM_001407302.1:c.2875_2878delinsGTG
NM_001407304.1:c.2152_2155delinsGTG
NM_001407305.1:c.2152_2155delinsGTG
NM_001407306.1:c.2152_2155delinsGTG
NM_001407307.1:c.1990_1993delinsGTG
NM_001407308.1:c.2152_2155delinsGTG
NM_001407309.1:c.2152_2155delinsGTG
NM_001407310.1:c.2152_2155delinsGTG
NM_001407311.1:c.2152_2155delinsGTG
NM_001407312.1:c.1249_1252delinsGTG
NM_001407313.1:c.1249_1252delinsGTG
NM_001407314.1:c.571_574delinsGTG
NM_024675.4:c.3037_3040delinsGTGMANE SELECT
NP_001394225.1:p.Ile993fs
NP_001394226.1:p.Ile989fs
NP_001394227.1:p.Ile959fs
NP_001394228.1:p.Ile1013fs
NP_001394230.1:p.Ile1013fs
NP_001394231.1:p.Ile959fs
NP_001394233.1:p.Ile718fs
NP_001394234.1:p.Ile718fs
NP_001394235.1:p.Ile718fs
NP_001394236.1:p.Ile664fs
NP_001394237.1:p.Ile718fs
NP_001394238.1:p.Ile718fs
NP_001394239.1:p.Ile718fs
NP_001394240.1:p.Ile718fs
NP_001394241.1:p.Ile417fs
NP_001394242.1:p.Ile417fs
NP_001394243.1:p.Ile191fs
NP_078951.2:p.Ile1013Valfs
NP_078951.2:p.Ile1013fs
LRG_308t1:c.3037_3040delATACinsGTG
LRG_308:g.24920_24923delinsGTG
LRG_308p1:p.Ile1013Valfs
NC_000016.9:g.23632756_23632759delinsCAC
NM_024675.3:c.3037_3040delATACinsGTG

Protein change:

I1013fs

Molecular consequence:

NM_001407296.1:c.2977_2980delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407297.1:c.2965_2968delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407298.1:c.2875_2878delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407299.1:c.3037_3040delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407301.1:c.3037_3040delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407302.1:c.2875_2878delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407304.1:c.2152_2155delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407305.1:c.2152_2155delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407306.1:c.2152_2155delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407307.1:c.1990_1993delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407308.1:c.2152_2155delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407309.1:c.2152_2155delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407310.1:c.2152_2155delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407311.1:c.2152_2155delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407312.1:c.1249_1252delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407313.1:c.1249_1252delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407314.1:c.571_574delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024675.4:c.3037_3040delinsGTG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407300.1:c.2834+2571_2834+2574delinsGTG - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004007926	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (May 19, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004007926

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(May 19, 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, SCV004007926.2

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

Description

The c.3037_3040delATACinsGTG pathogenic mutation, located in coding exon 10 of the PALB2 gene, results from the deletion of 4 nucleotides and insertion of 3 nucleotides causing a translational frameshift with a predicted alternate stop codon (p.I1013Vfs*2). 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 1, 2024

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