ClinVar Miner

Submissions for variant NM_002979.5(SCP2):c.825+1G>T

gnomAD frequency: 0.00009  dbSNP: rs144132787
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München RCV000578448 SCV000680368 likely pathogenic Sterol carrier protein 2 deficiency 2017-09-08 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001860007 SCV002281803 likely pathogenic not provided 2024-11-18 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 9 of the SCP2 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 SCP2 are known to be pathogenic (PMID: 16685654, 26497993). This variant is present in population databases (rs144132787, gnomAD 0.03%). Disruption of this splice site has been observed in individual(s) with clinical features of SCP2-related conditions (PMID: 33098801, 35872528). ClinVar contains an entry for this variant (Variation ID: 488590). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
PreventionGenetics, part of Exact Sciences RCV003409851 SCV004114359 pathogenic SCP2-related disorder 2022-08-24 criteria provided, single submitter clinical testing The SCP2 c.825+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant was reported in the homozygous state in an individual with adolescent onset dystonia (Table S2 - Zech et al. 2020. PubMed ID: 33098801). This variant is reported in 0.020% of alleles in individuals of European (Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-53444040-G-T). Variants that disrupt the consensus splice donor site in SCP2 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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