ClinVar Miner

Submissions for variant NM_025099.6(CTC1):c.2758+1G>T

gnomAD frequency: 0.00002  dbSNP: rs200609323
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000634497 SCV000755813 pathogenic Dyskeratosis congenita 2023-12-11 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 16 of the CTC1 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 CTC1 are known to be pathogenic (PMID: 22267198, 22387016). This variant is present in population databases (rs200609323, gnomAD 0.01%). Disruption of this splice site has been observed in individual(s) with cerebral microangiopathy with calcifications and cysts (PMID: 25197929). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 529185). 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.
Fulgent Genetics, Fulgent Genetics RCV000763024 SCV000893484 likely pathogenic Cerebroretinal microangiopathy with calcifications and cysts 1 2018-10-31 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000634497 SCV002531287 likely pathogenic Dyskeratosis congenita 2020-12-08 criteria provided, single submitter curation

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