ClinVar Miner

Submissions for variant NM_003126.4(SPTA1):c.3357G>C (p.Lys1119Asn)

gnomAD frequency: 0.00098  dbSNP: rs200230894
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 10
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000443048 SCV000536520 uncertain significance not provided 2017-01-20 criteria provided, single submitter clinical testing The K1119N variant in the SPTA1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The K1119N variant was not observed at any significant frequency in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The K1119N variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret K1119N as a variant of uncertain significance.
Illumina Laboratory Services, Illumina RCV001099386 SCV001255838 uncertain significance Elliptocytosis 2 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV001099387 SCV001255839 uncertain significance Pyropoikilocytosis, hereditary 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV001101374 SCV001257976 uncertain significance Hereditary spherocytosis type 3 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Centogene AG - the Rare Disease Company RCV001101374 SCV002028319 uncertain significance Hereditary spherocytosis type 3 2016-03-04 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000443048 SCV002505979 uncertain significance not provided 2022-01-26 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000443048 SCV002541196 uncertain significance not provided 2022-10-25 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000443048 SCV003822647 uncertain significance not provided 2023-12-04 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000443048 SCV004327631 benign not provided 2023-07-08 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004737490 SCV005350337 uncertain significance SPTA1-related disorder 2024-08-07 no assertion criteria provided clinical testing The SPTA1 c.3357G>C variant is predicted to result in the amino acid substitution p.Lys1119Asn. To our knowledge, this variant has not been reported in association with SPTA1-related disorders. This variant is reported in 0.11% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-158622275-C-G). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.