ClinVar Miner

Submissions for variant NM_001478.5(B4GALNT1):c.532-2A>G

dbSNP: rs1885117995
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001040708 SCV001204297 likely pathogenic Spastic paraplegia 2022-06-04 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 5 of the B4GALNT1 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 B4GALNT1 are known to be pathogenic (PMID: 23746551). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 839034). This variant has not been reported in the literature in individuals affected with B4GALNT1-related conditions. This variant is not present in population databases (gnomAD no frequency).
3billion, Medical Genetics RCV002051912 SCV002318781 pathogenic Hereditary spastic paraplegia 26 2022-03-22 criteria provided, single submitter clinical testing Canonical splice site: predicted to alter splicing and result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. This variant has been reported as pathogenic (ClinVar ID: VCV000839034). It is not observed in the gnomAD v2.1.1 dataset. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

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