NM_002485.5(NBN):c.2098C>A (p.Pro700Thr) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 28, 2020
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:: RCV001821291.4

Allele description [Variation Report for NM_002485.5(NBN):c.2098C>A (p.Pro700Thr)]

NM_002485.5(NBN):c.2098C>A (p.Pro700Thr)

Gene:

NBN:nibrin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q21.3

Genomic location:

Preferred name:

NM_002485.5(NBN):c.2098C>A (p.Pro700Thr)

HGVS:

NC_000008.11:g.89943339G>T
NG_008860.1:g.46333C>A
NM_001024688.3:c.1852C>A
NM_002485.5:c.2098C>AMANE SELECT
NP_001019859.1:p.Pro618Thr
NP_002476.2:p.Pro700Thr
NP_002476.2:p.Pro700Thr
LRG_158t1:c.2098C>A
LRG_158:g.46333C>A
LRG_158p1:p.Pro700Thr
NC_000008.10:g.90955567G>T
NM_002485.4:c.2098C>A

Protein change:

P618T

Links:

dbSNP: rs1060503461

NCBI 1000 Genomes Browser:

rs1060503461

Molecular consequence:

NM_001024688.3:c.1852C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002485.5:c.2098C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002064814	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 28, 2020)	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

SCV002064814

Genetic Services Laboratory, University of Chicago

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 28, 2020)

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	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV002064814.1

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

Description

DNA sequence analysis of the NBN gene demonstrated a sequence change, c.2098C>A, in exon 14 that results in an amino acid change, p.Pro700Thr. This sequence change does not appear to have been previously described in patients with NBN-related disorders and has been described in the gnomAD database in one individual with an overall population frequency of 0.0004% (dbSNP rs1060503461). The p.Pro700Thr change affects a highly conserved amino acid residue located in a domain of the NBN protein that is known to be functional. The p.Pro700Thr substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). Due to the lack of functional studies, the clinical significance of the p.Pro700Thr change remains unknown at this time.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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