ClinVar Miner

Submissions for variant NM_006415.4(SPTLC1):c.112CTT[1] (p.Leu39del)

dbSNP: rs1197928094
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV000988188 SCV001137822 likely pathogenic Neuropathy, hereditary sensory and autonomic, type 1A 2019-05-28 criteria provided, single submitter clinical testing
GeneDx RCV001560232 SCV001782597 likely pathogenic not provided 2019-08-14 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In-frame deletion of 1 amino acid in a non-repeat region; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 34059824)
Labcorp Genetics (formerly Invitae), Labcorp RCV001858688 SCV002213359 pathogenic Hereditary sensory and autonomic neuropathy type 1 2021-09-24 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this variant affects SPTLC1 function (PMID: 34059824). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. This variant has been observed in individual(s) with juvenile ALS (PMID: 34059824; Invitae). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (ExAC no frequency). This variant, c.115_117del, results in the deletion of 1 amino acid(s) of the SPTLC1 protein (p.Leu39del), but otherwise preserves the integrity of the reading frame.
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München RCV002468610 SCV002764914 likely pathogenic Proximal muscle weakness; Falls; Muscle spasm; EMG abnormality; Proximal lower limb amyotrophy 2022-03-01 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV001560232 SCV003819743 pathogenic not provided 2021-11-15 criteria provided, single submitter clinical testing
OMIM RCV003152613 SCV003841241 pathogenic Amyotrophic lateral sclerosis 27, juvenile 2023-03-16 no assertion criteria provided literature only
Solve-RD Consortium RCV000988188 SCV005200025 likely pathogenic Neuropathy, hereditary sensory and autonomic, type 1A 2022-06-01 no assertion criteria provided provider interpretation Variant confirmed as disease-causing by referring clinical team

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