ClinVar Miner

Submissions for variant NM_001023570.4(IQCB1):c.424_425del (p.Phe142fs) (rs750962965)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000001905 SCV000915984 pathogenic Senior-Loken syndrome 5 2017-04-28 criteria provided, single submitter clinical testing The IQCB1 c.424_425delTT (p.Phe142ProfsTer5) variant is a frameshift variant that is predicted to result in premature termination of the protein. The p.Phe142ProfsTer5 variant has been reported in three studies in which it is found in a total of nine individuals with Senior Loken syndrome, including in seven patients in a homozygous state and in two patients in a compound heterozygous state who both carried a null variant on the second allele (Otto et al. 2005; Estrada-Cuzcano et al. 2011; Halbritter et al. 2013). The p.Phe142ProfsTer5 variant was absent from 347 control subjects but is reported at a frequency of 0.00023 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the evidence, the p.Phe142ProfsTer5 variant is classified as pathogenic for Senior Loken syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Invitae RCV000822567 SCV000963376 pathogenic Nephronophthisis 2019-12-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Phe142Profs*5) in the IQCB1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs750962965, ExAC 0.02%). This variant has been reported in individuals affected with Leber congenital amaurosis and Senior-L ken syndrome (PMID: 23188109, 15723066, 28832562, 21866095, 20881296, 24625443, 28041643). This variant is also known as c.224_225delTT, p.F142fsX146 in the literature. ClinVar contains an entry for this variant (Variation ID: 1831). Loss-of-function variants in IQCB1 are known to be pathogenic (PMID: 15723066, 21866095). For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics RCV001073766 SCV001239326 pathogenic Retinal dystrophy 2017-12-06 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV001093170 SCV001250020 pathogenic not provided 2018-05-01 criteria provided, single submitter clinical testing
OMIM RCV000001905 SCV000022063 pathogenic Senior-Loken syndrome 5 2011-02-11 no assertion criteria provided literature only
NIHR Bioresource Rare Diseases, University of Cambridge RCV000505085 SCV000598854 pathogenic Leber congenital amaurosis 2015-01-01 no assertion criteria provided research
Human Genetics - Radboudumc,Radboudumc RCV000001905 SCV000804661 pathogenic Senior-Loken syndrome 5 2016-09-01 no assertion criteria provided clinical testing

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