ClinVar Miner

Submissions for variant NM_002528.7(NTHL1):c.350del (p.Pro117fs)

dbSNP: rs763525759
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV001021039 SCV001182602 pathogenic Hereditary cancer-predisposing syndrome 2021-05-13 criteria provided, single submitter clinical testing The c.374delC pathogenic mutation, located in coding exon 2 of the NTHL1 gene, results from a deletion of one nucleotide at nucleotide position 374, causing a translational frameshift with a predicted alternate stop codon (p.P125Qfs*12). 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV001382392 SCV001581143 pathogenic not provided 2024-09-23 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Pro125Glnfs*12) in the NTHL1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NTHL1 are known to be pathogenic (PMID: 25938944, 26559593). This variant is present in population databases (no rsID available, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with NTHL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 824156). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001382392 SCV001766833 likely pathogenic not provided 2023-12-26 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Myriad Genetics, Inc. RCV003458220 SCV004188358 pathogenic Familial adenomatous polyposis 3 2023-09-05 criteria provided, single submitter clinical testing This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.
Baylor Genetics RCV003458220 SCV004192176 likely pathogenic Familial adenomatous polyposis 3 2024-01-31 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV001382392 SCV004222200 likely pathogenic not provided 2022-08-24 criteria provided, single submitter clinical testing The NTHL1 c.374del (p.Pro125Glnfs*12) frameshift variant has not been reported in individuals with NTHL1-related diseases in the published literature. The frequency of this variant in the general population, 0.000085 (3/35378 chromosomes, http://gnomad.broadinstitute.org), is consistent with pathogenicity. Based on the available information, this variant is classified as likely pathogenic.
Fulgent Genetics, Fulgent Genetics RCV003458220 SCV005642824 likely pathogenic Familial adenomatous polyposis 3 2024-04-23 criteria provided, single submitter clinical testing

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