NM_000059.4(BRCA2):c.3563T>C (p.Ile1188Thr) AND Hereditary breast ovarian cancer syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 31, 2021
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:: RCV002024539.6

Allele description [Variation Report for NM_000059.4(BRCA2):c.3563T>C (p.Ile1188Thr)]

NM_000059.4(BRCA2):c.3563T>C (p.Ile1188Thr)

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.3563T>C (p.Ile1188Thr)

HGVS:

NC_000013.11:g.32337918T>C
NG_012772.3:g.27439T>C
NM_000059.4:c.3563T>CMANE SELECT
NP_000050.3:p.Ile1188Thr
LRG_293:g.27439T>C
NC_000013.10:g.32912055T>C
NM_000059.3:c.3563T>C

Protein change:

I1188T

Links:

dbSNP: rs2137497887

NCBI 1000 Genomes Browser:

rs2137497887

Molecular consequence:

NM_000059.4:c.3563T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary breast ovarian cancer syndrome
Synonyms:: Hereditary breast and ovarian cancer syndrome; Hereditary breast and ovarian cancer; Hereditary breast and ovarian cancer syndrome (HBOC); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0003582; MeSH: D061325; MedGen: C0677776; Orphanet: 145

Recent activity

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Mrps17-prov protein [Xenopus laevis]
Mrps17-prov protein [Xenopus laevis]
gi|32450598|gb|AAH54221.1|

Protein
CBSW3444.b1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8905224 5',...
CBSW3444.b1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8905224 5', mRNA sequence
gi|133759046|gnl|dbEST|45192241|gb| 301.1|

Nucleotide
CBTC10024.fwd NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8941091 5'...
CBTC10024.fwd NICHD_XGC_tropBone1 Xenopus tropicalis cDNA clone IMAGE:8941091 5', mRNA sequence
gi|126258212|gnl|dbEST|45032039|gb| 487.1|

Nucleotide
CBSW3630.g1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8905701 3',...
CBSW3630.g1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8905701 3', mRNA sequence
gi|133759342|gnl|dbEST|45192537|gb| 597.1|

Nucleotide
CBSW11584.b1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8912681 5'...
CBSW11584.b1 NICHD_XGC_tropTail_m Xenopus tropicalis cDNA clone IMAGE:8912681 5', mRNA sequence
gi|133770819|gnl|dbEST|45203740|gb| 800.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002316069	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 31, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002316069

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 31, 2021)

germline

clinical testing

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002316069.3

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

Description

This variant has not been reported in the literature in individuals with BRCA2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces isoleucine with threonine at codon 1188 of the BRCA2 protein (p.Ile1188Thr). The isoleucine residue is weakly conserved and there is a moderate physicochemical difference between isoleucine and threonine. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BRCA2 protein function.

#	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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