ClinVar Miner

Submissions for variant NM_023110.3(FGFR1):c.1825C>T (p.Arg609Ter)

dbSNP: rs121909639
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000478244 SCV000567333 pathogenic not provided 2015-09-08 criteria provided, single submitter clinical testing The R609X nonsense variant in the FGFR1 gene has been reported previously inassociation with Kallmann syndrome (Riley et al., 2007; Marcos et al., 2014). This variant is predicted to cause loss of normal protein function either through protein truncation ornonsense-mediated mRNA decay. Therefore, we consider the R609X variant to be pathogenic.
Genetic Services Laboratory, University of Chicago RCV000500417 SCV000594769 pathogenic Hypogonadotropic hypogonadism 2 with or without anosmia 2017-04-28 criteria provided, single submitter clinical testing
Reproductive Endocrine Unit, Massachusetts General Hospital RCV000500417 SCV003932494 pathogenic Hypogonadotropic hypogonadism 2 with or without anosmia 2023-05-04 criteria provided, single submitter research The variant NM_023110.2:c.1825C>T, p.(Arg609*) het has been classified as P1c based on the variant meeting the following ACMG Criteria: PVS1,PM2,PP3.
Labcorp Genetics (formerly Invitae), Labcorp RCV003764580 SCV004569644 pathogenic Hypogonadotropic hypogonadism 2 with or without anosmia; Pfeiffer syndrome 2023-07-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg609*) in the FGFR1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FGFR1 are known to be pathogenic (PMID: 12627230). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of Kallmann syndrome (PMID: 17360555). ClinVar contains an entry for this variant (Variation ID: 16296). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000030934 SCV000037966 risk factor Hypogonadotropic hypogonadism 2 with anosmia 2007-03-13 no assertion criteria provided literature only
Genomics England Pilot Project, Genomics England RCV000500417 SCV001760211 pathogenic Hypogonadotropic hypogonadism 2 with or without anosmia no assertion criteria provided clinical testing

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