ClinVar Miner

Submissions for variant NM_002485.5(NBN):c.265C>T (p.Arg89Ter)

gnomAD frequency: 0.00001  dbSNP: rs1057516320
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410234 SCV000485466 likely pathogenic Microcephaly, normal intelligence and immunodeficiency 2015-12-15 criteria provided, single submitter clinical testing
Invitae RCV000410234 SCV000758178 pathogenic Microcephaly, normal intelligence and immunodeficiency 2022-09-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg89*) in the NBN gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NBN are known to be pathogenic (PMID: 9590180, 16415040). This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with NBN-related conditions. ClinVar contains an entry for this variant (Variation ID: 370213). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV001782863 SCV002018218 pathogenic not provided 2019-04-02 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000410234 SCV002045370 pathogenic Microcephaly, normal intelligence and immunodeficiency 2021-11-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV001176293 SCV002744110 pathogenic Hereditary cancer-predisposing syndrome 2023-03-28 criteria provided, single submitter clinical testing The p.R89* pathogenic mutation (also known as c.265C>T), located in coding exon 3 of the NBN gene, results from a C to T substitution at nucleotide position 265. This changes the amino acid from an arginine to a stop codon within coding exon 3. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
Fulgent Genetics, Fulgent Genetics RCV002504201 SCV002817020 likely pathogenic Microcephaly, normal intelligence and immunodeficiency; Aplastic anemia; Acute lymphoid leukemia 2021-12-27 criteria provided, single submitter clinical testing
GeneDx RCV001782863 SCV004170247 likely pathogenic not provided 2023-06-06 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Observed in individuals with a personal and/or family history of breast and pancreatic cancer but also in cancer-free controls (Kotoula et al., 2017; Hu et al., 2018; Momozawa et al., 2018; Mizukami et al., 2020; Abe et al., 2021); This variant is associated with the following publications: (PMID: 30287823, 32980694, 9590180, 16415040, 28123851, 33413558, 29922827)
Baylor Genetics RCV003470325 SCV004199486 pathogenic Aplastic anemia 2023-10-31 criteria provided, single submitter clinical testing
Laboratory for Genotyping Development, RIKEN RCV003168586 SCV002758062 pathogenic Gastric cancer 2021-07-01 no assertion criteria provided research

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