ClinVar Miner

Submissions for variant NM_000264.5(PTCH1):c.318C>T (p.Leu106=)

gnomAD frequency: 0.01567  dbSNP: rs1805153
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000119167 SCV000153896 benign Gorlin syndrome 2024-02-01 criteria provided, single submitter clinical testing
Preventiongenetics, part of Exact Sciences RCV000253535 SCV000303346 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000119167 SCV000481350 benign Gorlin syndrome 2018-01-13 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Laboratory Services, Illumina RCV000265748 SCV000481351 benign Holoprosencephaly 7 2018-01-13 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Ambry Genetics RCV000492253 SCV000581017 benign Hereditary cancer-predisposing syndrome 2016-09-09 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000589609 SCV000604961 benign not provided 2023-11-07 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589609 SCV000696378 benign not provided 2016-05-24 criteria provided, single submitter clinical testing Variant summary: The PTCH1 c.318C>T (p.Leu106Leu) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predicting no significant impact on splicing and ESE finder predicting the elimination of an ESE binding site. However, these predictions have yet to be functionally assessed. The variant was observed in the large, broad control population, ExAC, with an allele frequency of 1737/120658 (10 homozygotes, 1/69, frequency: 0.0143961), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic PTCH1 variant of 1/58479 (0.0000171), suggesting this variant is likely a benign polymorphism. The variant has been reported in affected individuals via publications and/or reputable clinical laboratories with a classification of "polymorphism/benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000253535 SCV002046721 benign not specified 2021-03-16 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002492406 SCV002798105 likely benign Basal cell carcinoma, susceptibility to, 1; Gorlin syndrome; Holoprosencephaly 7 2022-03-29 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000119167 SCV004017148 benign Gorlin syndrome 2023-07-07 criteria provided, single submitter clinical testing

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