ClinVar Miner

Submissions for variant NM_000234.3(LIG1):c.1244del (p.Thr415fs)

gnomAD frequency: 0.00001  dbSNP: rs778319960
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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 RCV002545232 SCV003472618 pathogenic not provided 2024-01-03 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Thr415Metfs*10) in the LIG1 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in LIG1 cause disease. This variant is present in population databases (rs778319960, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with DNA ligase I deficiency (PMID: 30395541). 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: 1343095). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects LIG1 function (PMID: 30395541). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV001843697 SCV002102819 pathogenic Immunodeficiency 96 2022-03-07 no assertion criteria provided literature only

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