NM_024675.4(PALB2):c.3089C>G (p.Thr1030Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 22, 2022
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:: RCV003182740.2

Allele description [Variation Report for NM_024675.4(PALB2):c.3089C>G (p.Thr1030Ser)]

NM_024675.4(PALB2):c.3089C>G (p.Thr1030Ser)

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.3089C>G (p.Thr1030Ser)

HGVS:

NC_000016.10:g.23621386G>C
NG_007406.1:g.24972C>G
NM_001407296.1:c.3029C>G
NM_001407297.1:c.3017C>G
NM_001407298.1:c.2927C>G
NM_001407299.1:c.3089C>G
NM_001407300.1:c.2834+2623C>G
NM_001407301.1:c.3089C>G
NM_001407302.1:c.2927C>G
NM_001407304.1:c.2204C>G
NM_001407305.1:c.2204C>G
NM_001407306.1:c.2204C>G
NM_001407307.1:c.2042C>G
NM_001407308.1:c.2204C>G
NM_001407309.1:c.2204C>G
NM_001407310.1:c.2204C>G
NM_001407311.1:c.2204C>G
NM_001407312.1:c.1301C>G
NM_001407313.1:c.1301C>G
NM_001407314.1:c.623C>G
NM_024675.4:c.3089C>GMANE SELECT
NP_001394225.1:p.Thr1010Ser
NP_001394226.1:p.Thr1006Ser
NP_001394227.1:p.Thr976Ser
NP_001394228.1:p.Thr1030Ser
NP_001394230.1:p.Thr1030Ser
NP_001394231.1:p.Thr976Ser
NP_001394233.1:p.Thr735Ser
NP_001394234.1:p.Thr735Ser
NP_001394235.1:p.Thr735Ser
NP_001394236.1:p.Thr681Ser
NP_001394237.1:p.Thr735Ser
NP_001394238.1:p.Thr735Ser
NP_001394239.1:p.Thr735Ser
NP_001394240.1:p.Thr735Ser
NP_001394241.1:p.Thr434Ser
NP_001394242.1:p.Thr434Ser
NP_001394243.1:p.Thr208Ser
NP_078951.2:p.Thr1030Ser
NP_078951.2:p.Thr1030Ser
LRG_308t1:c.3089C>G
LRG_308:g.24972C>G
LRG_308p1:p.Thr1030Ser
NC_000016.9:g.23632707G>C
NM_024675.3:c.3089C>G

Protein change:

T1006S

Molecular consequence:

NM_001407300.1:c.2834+2623C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407296.1:c.3029C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407297.1:c.3017C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407298.1:c.2927C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407299.1:c.3089C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407301.1:c.3089C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407302.1:c.2927C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407304.1:c.2204C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407305.1:c.2204C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407306.1:c.2204C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407307.1:c.2042C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407308.1:c.2204C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407309.1:c.2204C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407310.1:c.2204C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407311.1:c.2204C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407312.1:c.1301C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407313.1:c.1301C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407314.1:c.623C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_024675.4:c.3089C>G - 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
SCV003867654	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Nov 22, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003867654

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Nov 22, 2022)

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, SCV003867654.2

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

Description

The p.T1030S variant (also known as c.3089C>G), located in coding exon 10 of the PALB2 gene, results from a C to G substitution at nucleotide position 3089. The threonine at codon 1030 is replaced by serine, an amino acid with 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: May 1, 2024

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