NM_000059.4(BRCA2):c.4016G>T (p.Ser1339Ile) AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Mar 23, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV002359452.6

Allele description [Variation Report for NM_000059.4(BRCA2):c.4016G>T (p.Ser1339Ile)]

NM_000059.4(BRCA2):c.4016G>T (p.Ser1339Ile)

Gene:

BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.4(BRCA2):c.4016G>T (p.Ser1339Ile)

HGVS:

NC_000013.11:g.32338371G>T
NG_012772.3:g.27892G>T
NM_000059.4:c.4016G>TMANE SELECT
NM_001406719.1:c.4016G>T
NM_001406720.1:c.4016G>T
NP_000050.2:p.Ser1339Ile
NP_000050.3:p.Ser1339Ile
NP_001393648.1:p.Ser1339Ile
NP_001393649.1:p.Ser1339Ile
LRG_293t1:c.4016G>T
LRG_293:g.27892G>T
LRG_293p1:p.Ser1339Ile
NC_000013.10:g.32912508G>T
NM_000059.3:c.4016G>T
NR_176251.1:n.4215G>T

Protein change:

S1339I

Molecular consequence:

NM_000059.4:c.4016G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406719.1:c.4016G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406720.1:c.4016G>T - 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

Recent activity

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Homo sapiens FAT tumor suppressor homolog 4 (Drosophila) (FAT4), mRNA
Homo sapiens FAT tumor suppressor homolog 4 (Drosophila) (FAT4), mRNA
gi|47059029|ref|NM_024582.2|

Nucleotide
Homo sapiens vacuolar protein sorting 11 homolog (S. cerevisiae), mRNA (cDNA clo...
Homo sapiens vacuolar protein sorting 11 homolog (S. cerevisiae), mRNA (cDNA clone MGC:74765 IMAGE:6144541), complete cds
gi|41388979|gb|BC065563.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002620825	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Mar 17, 2020)	germline	clinical testing	Citation Link,
SCV003848608	University of Washington Department of Laboratory Medicine, University of Washington	criteria provided, single submitter (Dines et al. (Genet Med. 2020))	Likely benign (Mar 23, 2023)	germline	curation	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002620825

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Mar 17, 2020)

germline

clinical testing

Citation Link,

SCV003848608

University of Washington Department of Laboratory Medicine, University of Washington

criteria provided, single submitter

(Dines et al. (Genet Med. 2020))

Likely benign
(Mar 23, 2023)

germline

curation

PubMed (1)
[See all records that cite this PMID]

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, curation

Citations

PubMed

Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".

Dines JN, Shirts BH, Slavin TP, Walsh T, King MC, Fowler DM, Pritchard CC.

Genet Med. 2020 May;22(5):825-830. doi: 10.1038/s41436-019-0740-6. Epub 2020 Jan 8.

PubMed [citation]

PMID:: 31911673
PMCID:: PMC7200594

Details of each submission

From Ambry Genetics, SCV002620825.2

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

Description

The p.S1339I variant (also known as c.4016G>T), located in coding exon 10 of the BRCA2 gene, results from a G to T substitution at nucleotide position 4016. The serine at codon 1339 is replaced by isoleucine, an amino acid with dissimilar properties. This amino acid position is not well conserved in available vertebrate species. 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

From University of Washington Department of Laboratory Medicine, University of Washington, SCV003848608.1

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

Description

Missense variant in a coldspot region where missense variants are very unlikely to be pathogenic (PMID:31911673).

#	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 1, 2024

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