ClinVar Miner

Submissions for variant NM_022455.5(NSD1):c.6013C>T (p.Arg2005Ter)

dbSNP: rs587784173
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV003231293 SCV000194231 pathogenic Sotos syndrome 2013-02-08 criteria provided, single submitter clinical testing
GeneDx RCV000255064 SCV000322461 pathogenic not provided 2022-06-01 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 in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 15942875, 28475857, 33084842, 14571271, 34008892)
Labcorp Genetics (formerly Invitae), Labcorp RCV000255064 SCV000828105 pathogenic not provided 2019-10-28 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in NSD1 are known to be pathogenic (PMID: 12464997, 14571271, 15942875, 16247291). This variant has been reported to be de novo in an individual affected with Sotos syndrome (PMID: 14571271). This variant has been observed in individuals affected with learning disability, overgrowth, and/or sacrococcygeal teratoma (PMID: 15942875, 28475857). ClinVar contains an entry for this variant (Variation ID: 159394). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Arg2005*) in the NSD1 gene. It is expected to result in an absent or disrupted protein product.
Laboratory of Medical Genetics, National & Kapodistrian University of Athens RCV003231293 SCV000928345 pathogenic Sotos syndrome 2018-02-15 criteria provided, single submitter clinical testing PVS1, PM1, PM2, PP3, PP5
Revvity Omics, Revvity RCV003231293 SCV002020557 pathogenic Sotos syndrome 2020-11-20 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003231293 SCV002054961 pathogenic Sotos syndrome 2021-07-15 criteria provided, single submitter clinical testing
MGZ Medical Genetics Center RCV003231293 SCV002579166 pathogenic Sotos syndrome 2022-05-06 criteria provided, single submitter clinical testing
Neuberg Centre For Genomic Medicine, NCGM RCV003231293 SCV005060902 pathogenic Sotos syndrome criteria provided, single submitter clinical testing The observed stop gained variant c.6013C>T(p.Arg2005Ter) in NSD1 gene has been reported previously in heterozygous state in multiple individuals with Sotos syndorme (Tatton-Brown K, et al., 2017; 2005, Türkmen S, et al., 2003). The variant c.6013C>T is absent in gnomAD Exomes. This variant has been reported to the ClinVar database as Likely Pathogenic/Pathogenic (multiple submissions). This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic.
Genomics England Pilot Project, Genomics England RCV003231293 SCV001760159 likely pathogenic Sotos syndrome no assertion criteria provided clinical testing

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