NM_002485.5(NBN):c.1690G>A (p.Glu564Lys) AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Jun 10, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000129092.14

Allele description [Variation Report for NM_002485.5(NBN):c.1690G>A (p.Glu564Lys)]

NM_002485.5(NBN):c.1690G>A (p.Glu564Lys)

Gene:

NBN:nibrin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q21.3

Genomic location:

Preferred name:

NM_002485.5(NBN):c.1690G>A (p.Glu564Lys)

Other names:

p.E564K:GAA>AAA

HGVS:

NC_000008.11:g.89953399C>T
NG_008860.1:g.36273G>A
NM_001024688.3:c.1444G>A
NM_002485.5:c.1690G>AMANE SELECT
NP_001019859.1:p.Glu482Lys
NP_002476.2:p.Glu564Lys
NP_002476.2:p.Glu564Lys
LRG_158t1:c.1690G>A
LRG_158:g.36273G>A
LRG_158p1:p.Glu564Lys
NC_000008.10:g.90965627C>T
NM_002485.4:c.1690G>A
p.E564K

Protein change:

E482K

Links:

dbSNP: rs72550742

NCBI 1000 Genomes Browser:

rs72550742

Molecular consequence:

NM_001024688.3:c.1444G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002485.5:c.1690G>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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Slc29a3 solute carrier family 29 (nucleoside transporters), member 3 [Mus muscul...
Slc29a3 solute carrier family 29 (nucleoside transporters), member 3 [Mus musculus]
Gene ID:71279

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000183802	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Sep 27, 2018)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 24349281, 25712764, 25980754 Citation Link,
SCV002536614	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Benign (Jun 10, 2020)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000183802

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Sep 27, 2018)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link,

SCV002536614

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Benign
(Jun 10, 2020)

germline

curation

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, curation

Citations

PubMed

Mutation inactivation of Nijmegen breakage syndrome gene (NBS1) in hepatocellular carcinoma and intrahepatic cholangiocarcinoma.

Wang Y, Hong Y, Li M, Long J, Zhao YP, Zhang JX, Li Q, You H, Tong WM, Jia JD, Huang J.

PLoS One. 2013;8(12):e82426. doi: 10.1371/journal.pone.0082426.

PubMed [citation]

PMID:: 24349281
PMCID:: PMC3862623

Heterozygous germline mutations in NBS1 among Korean patients with high-risk breast cancer negative for BRCA1/2 mutation.

Kim H, Cho DY, Choi DH, Jung GH, Shin I, Park W, Huh SJ, Kim SW, Park SK, Lee JW, Nam SJ, Lee JE, Gil WH, Kim SW.

Fam Cancer. 2015 Sep;14(3):365-71. doi: 10.1007/s10689-015-9789-9.

PubMed [citation]

PMID:: 25712764

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV000183802.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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 Sema4, Sema4, SCV002536614.1

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

#	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: Oct 20, 2024

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