ClinVar Miner

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

dbSNP: rs1568579997
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000796674 SCV000936197 likely pathogenic MHC class II deficiency 2019-12-11 criteria provided, single submitter clinical testing 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. Loss-of-function variants in RFXANK are known to be pathogenic (PMID: 10803838, 16166641, 21908431). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant has not been reported in the literature in individuals with RFXANK-related disease. ClinVar contains an entry for this variant (Variation ID: 643059). This variant is not present in population databases (ExAC no frequency). This variant is a deletion of the genomic region encompassing part of exon 6 (c.419_438+38del) of the RFXANK gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.
PreventionGenetics, part of Exact Sciences RCV003411751 SCV004106334 likely pathogenic RFXANK-related condition 2023-12-08 criteria provided, single submitter 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.
OMIM RCV002291217 SCV000027173 pathogenic Bare lymphocyte syndrome, type II, complementation group B 1998-11-01 no assertion criteria provided literature only

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