NM_032043.3(BRIP1):c.260G>A (p.Cys87Tyr) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 11, 2019
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:: RCV000200543.9

Allele description [Variation Report for NM_032043.3(BRIP1):c.260G>A (p.Cys87Tyr)]

NM_032043.3(BRIP1):c.260G>A (p.Cys87Tyr)

Gene:

BRIP1:BRCA1 interacting DNA helicase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q23.2

Genomic location:

Preferred name:

NM_032043.3(BRIP1):c.260G>A (p.Cys87Tyr)

HGVS:

NC_000017.11:g.61857177C>T
NG_007409.2:g.11383G>A
NM_032043.3:c.260G>AMANE SELECT
NP_114432.2:p.Cys87Tyr
NP_114432.2:p.Cys87Tyr
LRG_300t1:c.260G>A
LRG_300:g.11383G>A
LRG_300p1:p.Cys87Tyr
NC_000017.10:g.59934538C>T
NM_032043.2:c.260G>A

Protein change:

C87Y

Links:

dbSNP: rs863224800

NCBI 1000 Genomes Browser:

rs863224800

Molecular consequence:

NM_032043.3:c.260G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial cancer of breast
Synonyms:: Breast cancer, familial; Hereditary breast cancer
Identifiers:: MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480

Name:: Fanconi anemia complementation group J
Identifiers:: MONDO: MONDO:0012187; MedGen: C1836860; Orphanet: 84; OMIM: 609054

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Homo sapiens SMAD family member 9 (SMAD9), transcript variant b, mRNA
Homo sapiens SMAD family member 9 (SMAD9), transcript variant b, mRNA
gi|1677537860|ref|NM_005905.6|

Nucleotide
JGI_XZT7130.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7585474 5',...
JGI_XZT7130.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7585474 5', mRNA sequence
gi|57054001|gnl|dbEST|26940415|gb|C 51.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000255158	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 11, 2019)	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

SCV000255158

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 11, 2019)

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, SCV000255158.6

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

Description

In summary, this is a novel missense change that is not predicted to affect protein function or cause disease. However the evidence is insufficient at this time to prove that conclusively. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies. This variant has not been published in the literature and is not present in population databases. ClinVar contains an entry for this variant (Variation ID: 216790). This sequence change replaces cysteine with tyrosine at codon 87 of the BRIP1 protein (p.Cys87Tyr). The cysteine residue is moderately conserved and there is a large physicochemical difference between cysteine and tyrosine.

#	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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