NM_024675.4(PALB2):c.407G>A (p.Ser136Asn) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 10, 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:: RCV004374086.1

Allele description [Variation Report for NM_024675.4(PALB2):c.407G>A (p.Ser136Asn)]

NM_024675.4(PALB2):c.407G>A (p.Ser136Asn)

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.407G>A (p.Ser136Asn)

HGVS:

NC_000016.10:g.23636139C>T
NG_007406.1:g.10219G>A
NM_001407296.1:c.347G>A
NM_001407297.1:c.407G>A
NM_001407298.1:c.407G>A
NM_001407299.1:c.407G>A
NM_001407300.1:c.407G>A
NM_001407301.1:c.407G>A
NM_001407302.1:c.407G>A
NM_001407304.1:c.-479G>A
NM_001407305.1:c.-479G>A
NM_001407306.1:c.-479G>A
NM_001407307.1:c.-479G>A
NM_001407308.1:c.-479G>A
NM_001407309.1:c.-479G>A
NM_001407310.1:c.-479G>A
NM_001407311.1:c.-479G>A
NM_001407312.1:c.-105+4971G>A
NM_001407313.1:c.-105+4971G>A
NM_001407314.1:c.48+4971G>A
NM_024675.4:c.407G>AMANE SELECT
NP_001394225.1:p.Ser116Asn
NP_001394226.1:p.Ser136Asn
NP_001394227.1:p.Ser136Asn
NP_001394228.1:p.Ser136Asn
NP_001394229.1:p.Ser136Asn
NP_001394230.1:p.Ser136Asn
NP_001394231.1:p.Ser136Asn
NP_078951.2:p.Ser136Asn
NP_078951.2:p.Ser136Asn
LRG_308t1:c.407G>A
LRG_308:g.10219G>A
LRG_308p1:p.Ser136Asn
NC_000016.9:g.23647460C>T
NM_024675.3:c.407G>A

Protein change:

S116N

Molecular consequence:

NM_001407304.1:c.-479G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407305.1:c.-479G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407306.1:c.-479G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407307.1:c.-479G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407308.1:c.-479G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407309.1:c.-479G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407310.1:c.-479G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407311.1:c.-479G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407312.1:c.-105+4971G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407313.1:c.-105+4971G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407314.1:c.48+4971G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407296.1:c.347G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407297.1:c.407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407298.1:c.407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407299.1:c.407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407300.1:c.407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407301.1:c.407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407302.1:c.407G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024675.4:c.407G>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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005029090	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Dec 10, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005029090

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Dec 10, 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, SCV005029090.1

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

Description

The p.S136N variant (also known as c.407G>A), located in coding exon 4 of the PALB2 gene, results from a G to A substitution at nucleotide position 407. The serine at codon 136 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: Sep 29, 2024

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