NM_001077494.3(NFKB2):c.2609G>A (p.Ser870Asn) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Jun 30, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000484648.1

Allele description [Variation Report for NM_001077494.3(NFKB2):c.2609G>A (p.Ser870Asn)]

NM_001077494.3(NFKB2):c.2609G>A (p.Ser870Asn)

Gene:
NFKB2:nuclear factor kappa B subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q24.32
Genomic location:
Preferred name:
NM_001077494.3(NFKB2):c.2609G>A (p.Ser870Asn)
HGVS:
  • NC_000010.11:g.102402282G>A
  • NG_033874.1:g.13173G>A
  • NM_001077494.3:c.2609G>A
  • NM_001288724.1:c.2606G>A
  • NM_001322934.1:c.2609G>A
  • NP_001070962.1:p.Ser870Asn
  • NP_001275653.1:p.Ser869Asn
  • NP_001309863.1:p.Ser870Asn
  • NC_000010.10:g.104162039G>A
Protein change:
S869N
Links:
dbSNP: rs1064795232
NCBI 1000 Genomes Browser:
rs1064795232
Molecular consequence:
  • NM_001288724.1:c.2606G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000570847GeneDxcriteria provided, single submitter
Likely pathogenic
(Jun 30, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000570847.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The S870N variant in the NFKB2 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The S870N variant was not observed in approximately 6200 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The S870N variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Missense variants in nearby residues (D865G, A867V) have been reported in the Human Gene Mutation Database in association with common variable immunodeficiency (Stenson et al., 2014), supporting the functional importance of this region of the protein. Therefore, we interpret S870N as a likely pathogenic variant

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 17, 2019

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