ClinVar Miner

Submissions for variant NM_001256789.3(CACNA1F):c.2543+1G>A

gnomAD frequency: 0.00001  dbSNP: rs886044841
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000360556 SCV000338397 pathogenic not provided 2016-01-25 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000360556 SCV001228194 pathogenic not provided 2024-10-01 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 20 of the CACNA1F 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 CACNA1F are known to be pathogenic (PMID: 9662399, 11281458, 17525176, 22194652, 24124559, 26992781). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with congenital stationary night blindness (PMID: 22183355, 28838317, 30825406). ClinVar contains an entry for this variant (Variation ID: 285396). 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 RCV002502130 SCV002784728 pathogenic Aland island eye disease; X-linked cone-rod dystrophy 3; Congenital stationary night blindness 2A 2021-09-10 criteria provided, single submitter clinical testing
GeneDx RCV000360556 SCV005078813 pathogenic not provided 2024-03-25 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 28838317, 30825406, 22183355, 33668843)
PreventionGenetics, part of Exact Sciences RCV003417898 SCV004116755 pathogenic CACNA1F-related disorder 2024-07-22 no assertion criteria provided clinical testing The CACNA1F c.2576+1G>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported in multiple individuals with congenital stationary night blindness (Wang et al. 2017. PubMed ID: 28838317; Zeitz et al. 2019. PubMed ID: 30825406; Lodha et al. 2012. PubMed ID: 22183355; Leahy et al. 2021. PubMed ID: 33668843). This variant is reported in 0.0014% of alleles in individuals of European (non-Finnish) descent in gnomAD. Variants that disrupt the consensus splice donor site in CACNA1F are expected to be pathogenic. This variant is interpreted as pathogenic.

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