ClinVar Miner

Submissions for variant NM_003721.4(RFXANK):c.419_438+38del

dbSNP: rs1568579997
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 3
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000796674 SCV000936197 likely pathogenic MHC class II deficiency 2024-09-19 criteria provided, single submitter clinical testing This variant results in the deletion of part of exon 6 (c.419_438+38del) of the RFXANK 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 RFXANK are known to be pathogenic (PMID: 10803838, 16166641, 21908431). 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. This variant has been observed in individual(s) with MHC class II deficiency (PMID: 9806546). ClinVar contains an entry for this variant (Variation ID: 643059). 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.
OMIM RCV004576969 SCV000027173 pathogenic MHC class II deficiency 2 1998-11-01 no assertion criteria provided literature only
PreventionGenetics, part of Exact Sciences RCV003411751 SCV004106334 likely pathogenic RFXANK-related disorder 2023-12-08 no assertion criteria provided clinical testing The RFXANK c.419_438+38del58 variant is predicted to result in a deletion affecting a canonical splice site. This variant has been reported in individuals with major histocompatibility class II deficiency, also referred to as bare lymphocyte syndrome, complementation group B (Masternak et al. 1998. PubMed ID: 9806546; Supplemental Table 3, Farwell et al. 2014. PubMed ID: 25356970). This variant is reported in 0.0023% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Frameshift variants in RFXANK are expected to be pathogenic. This variant is interpreted as likely pathogenic.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.