ClinVar Miner

Submissions for variant NM_006017.3(PROM1):c.1984-1G>T

gnomAD frequency: 0.00001  dbSNP: rs373680665
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV000987420 SCV001136710 pathogenic Retinitis pigmentosa 41 2019-05-28 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001049161 SCV001213195 pathogenic not provided 2025-01-06 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 17 of the PROM1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PROM1 are known to be pathogenic (PMID: 17605048, 19718270, 24154662, 25474345). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. Disruption of this splice site has been observed in individuals with autosomal recessive PROM1-related retinal dystrophy (PMID: 24516651, 31129250). ClinVar contains an entry for this variant (Variation ID: 802053). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
DBGen Ocular Genomics RCV000987420 SCV001815932 pathogenic Retinitis pigmentosa 41 2021-06-21 criteria provided, single submitter clinical testing
Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel RCV003324540 SCV004030438 pathogenic Cone-rod dystrophy 2023-07-24 criteria provided, single submitter research Clinical significance based on ACMG v2.0
Ophthalmic Genetics Group, Institute of Molecular and Clinical Ophthalmology Basel RCV003324541 SCV004030439 pathogenic Leber congenital amaurosis 2023-07-24 criteria provided, single submitter research Clinical significance based on ACMG v2.0
PreventionGenetics, part of Exact Sciences RCV004536013 SCV004113255 pathogenic PROM1-related disorder 2023-08-08 criteria provided, single submitter clinical testing The PROM1 c.1984-1G>T variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant been reported in multiple individuals with autosomal recessive retinitis pigmentosa (de Castro-Miró et al 2014. PubMed ID: 24516651) and autosomal recessive cone-rod dystrophy (Del Pozo-Valero M et al 2019. PubMed ID: 31129250). This variant is reported in 0.0095% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/4-15991448-C-A). Variants that disrupt the consensus splice acceptor site in PROM1 are expected to be pathogenic. This variant is interpreted as pathogenic.
Ophthalmo-Genetics Lab, Instituto de Oftalmologia Conde de Valenciana RCV002467454 SCV002762718 pathogenic Stargardt disease 2022-12-14 no assertion criteria provided research

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