ClinVar Miner

Submissions for variant NM_003640.5(ELP1):c.2824C>T (p.Arg942Ter)

gnomAD frequency: 0.00001  dbSNP: rs761911009
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001052645 SCV001216866 pathogenic not provided 2024-01-09 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg942*) in the ELP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ELP1 are known to be pathogenic (PMID: 18303054, 24173031). This variant is present in population databases (rs761911009, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with ELP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 848810). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV004031649 SCV002754963 pathogenic not specified 2019-09-17 criteria provided, single submitter clinical testing The p.R942* pathogenic mutation (also known as c.2824C>T), located in coding exon 25 of the IKBKAP gene, results from a C to T substitution at nucleotide position 2824. This changes the amino acid from an arginine to a stop codon within coding exon 25. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
Fulgent Genetics, Fulgent Genetics RCV002505601 SCV002795884 likely pathogenic Medulloblastoma; Familial dysautonomia 2021-12-20 criteria provided, single submitter clinical testing
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV003444766 SCV004171533 pathogenic Medulloblastoma 2023-10-16 criteria provided, single submitter clinical testing The ELP1 c.2824C>T (p.Arg942Ter) change is a nonsense variant that is predicted to cause premature protein truncation or absence of protein due to nonsense-mediated decay. This variant has been reported in an individual with the sonic hedgehog (SHH) subtype of medulloblastoma (internal data). This variant has a maximum subpopulation frequency of 0.01% in gnomAD v2.1.1 (https:// gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as pathogenic.

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