ClinVar Miner

Submissions for variant NM_004722.4(AP4M1):c.52_58+6del

dbSNP: rs1350685858
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002019358 SCV002285426 pathogenic Hereditary spastic paraplegia 50 2022-09-13 criteria provided, single submitter clinical testing This variant is not present in population databases (gnomAD no frequency). This variant results in the deletion of part of exon 1 (c.52_58+6del) of the AP4M1 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 AP4M1 are known to be pathogenic (PMID: 24700674, 25496299, 25558065). This variant has been observed in individual(s) with clinical features of AP4M1-related conditions (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1497146). 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.

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