ClinVar Miner

Submissions for variant NM_001126049.2(KLLN):c.-1007C>G (rs587780001)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PTEN Variant Curation Expert Panel RCV000790889 SCV000930123 likely benign PTEN hamartoma tumor syndrome 2019-06-25 reviewed by expert panel curation PTEN c.-975G>C (g.89623251G>C) meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the "PTEN ACMG Specifications Summary" document (assertion method column). BS1: Allele frequency of 0.006 (0.6%, 21/3466 alleles) in the European (Finnish) subpopulation and 0.002 (0.2%, 30/14,976) in the European (Non-Finnish) subpopulation of the gnomAD cohort. (PMID 27535533) BP5: Variant found in multiple cases with alternate molecular basis for disease. (internal laboratory contributors SCV000187238.1, SCV000149489.5)
GeneDx RCV000252011 SCV000149489 uncertain significance not specified 2016-12-15 criteria provided, single submitter clinical testing This variant is denoted PTEN c.-976G>C, and describes a nucleotide substitution 976 base pairs upstream of the ATG translational start site in the PTEN promoter region. The surrounding sequence, with the base that is substituted in braces, is CCTC{G/C}GTCT, and is also called c.-975G>C using alternate numbering. This variant was observed in a case of hereditary prostate cancer (Xie 2011). Variants within the PTEN promoter have been observed in individuals with features of Cowden syndrome (Zhou 2003). Based on currently available information, it is unclear whether PTEN c.-976G>C is pathogenic or benign. We consider it to be a variant of uncertain significance.
Ambry Genetics RCV000115580 SCV000187238 uncertain significance Hereditary cancer-predisposing syndrome 2014-05-05 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000252011 SCV000303566 uncertain significance not specified criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589059 SCV000696555 benign not provided 2017-05-26 criteria provided, single submitter clinical testing Variant summary: The PTEN c.-975G>C (also known as c.-976G>C) variant involves the alteration of a non-conserved nucleotide in 5'UTR. One in silico tool predicts a benign outcome for this variant. This variant was found in 55/30846 control chromosomes at a frequency of 0.0017831, which is approximately 285 times the estimated maximal expected allele frequency of a pathogenic PTEN variant (0.0000063), suggesting this variant is likely a benign polymorphism. Although multiple clinical diagnostic laboratories classified this variant as uncertain significance, this variant is classified as benign due to its relatively high frequency in controls.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000589059 SCV001148034 uncertain significance not provided 2018-06-01 criteria provided, single submitter clinical testing
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital RCV000781947 SCV000920390 uncertain significance Seizures 2017-08-16 no assertion criteria provided clinical testing

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