ClinVar Miner

Submissions for variant NM_023110.3(FGFR1):c.1864C>T (p.Arg622Ter)

dbSNP: rs121909628
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Chan Lab, Boston Children's Hospital RCV000156953 SCV000206674 likely pathogenic Hypogonadotropic hypogonadism 7 with or without anosmia 2014-11-01 criteria provided, single submitter case-control
Chan Lab, Boston Children's Hospital RCV000156954 SCV000206675 likely pathogenic Delayed puberty 2014-11-01 criteria provided, single submitter case-control
GeneDx RCV000760399 SCV000890272 pathogenic not provided 2018-11-13 criteria provided, single submitter clinical testing The R622X nonsense variant has been reported previously in association with FGFR1-related disorders (Dodé et al., 2003; Pitteloud et al., 2005). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The variant is not observed in large population cohorts (Lek et al., 2016). We consider this variant to be pathogenic.
Institute of Human Genetics, University Hospital Muenster RCV004584329 SCV002054131 pathogenic See cases 2021-02-12 criteria provided, single submitter clinical testing ACMG categories: PVS1,PM2,PP3,PP5
Labcorp Genetics (formerly Invitae), Labcorp RCV002513084 SCV003440845 pathogenic Hypogonadotropic hypogonadism 2 with or without anosmia; Pfeiffer syndrome 2023-09-12 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 16282). This premature translational stop signal has been observed in individual(s) with autosomal dominant FGFR1-related conditions (PMID: 12627230, 17200176, 25636053, 32853167, 33548149). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg622*) 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).
Reproductive Endocrine Unit, Massachusetts General Hospital RCV000030926 SCV003932498 pathogenic Hypogonadotropic hypogonadism 2 with or without anosmia 2023-05-04 criteria provided, single submitter research The variant NM_023110.2:c.1864C>T, p.(Arg622*) het has been classified as P1c based on the variant meeting the following ACMG Criteria: PVS1,PM2,PP3.
OMIM RCV000030926 SCV000037950 risk factor Hypogonadotropic hypogonadism 2 with or without anosmia 2007-03-01 no assertion criteria provided literature only
Genomics England Pilot Project, Genomics England RCV000030926 SCV001760210 pathogenic Hypogonadotropic hypogonadism 2 with or without anosmia no assertion criteria provided clinical testing

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