ClinVar Miner

Submissions for variant NM_001369369.1(FOXN1):c.1135+1_1135+2delinsAG

dbSNP: rs1064795660
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000480185 SCV000571673 likely pathogenic not provided 2016-09-13 criteria provided, single submitter clinical testing The c.1135+1_1135+2delGTinsAG splice site variant in the FOXN1 gene destroys the canonical splice donor site in intron 6. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. However, very few variants in this gene have been published, and no splicing variant has been published in the Human Gene Mutation Database in association with disease (Stenson et al., 2014). Therefore, we consider this variant to be likely pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV002526627 SCV003317806 likely pathogenic T-cell immunodeficiency, congenital alopecia, and nail dystrophy 2022-03-04 criteria provided, single submitter clinical testing This sequence change affects a splice site in intron 6 of the FOXN1 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 FOXN1 are known to be pathogenic (PMID: 10206641, 15180707, 31447097). 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. ClinVar contains an entry for this variant (Variation ID: 422253). This variant has not been reported in the literature in individuals affected with FOXN1-related conditions. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database.

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