ClinVar Miner

Submissions for variant NM_002769.5(PRSS1):c.390C>T (p.Thr130=)

gnomAD frequency: 0.00012  dbSNP: rs561097415
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000149415 SCV000630746 likely benign Hereditary pancreatitis 2024-02-20 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590793 SCV000698047 benign not provided 2017-04-25 criteria provided, single submitter clinical testing Variant summary: The PRSS1 c.390C>T (p.Thr130Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool (mutation taster) predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect multiple ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 28/120840 control chromosomes from ExAC at a frequency of 0.0002317, which is approximately 46 times the estimated maximal expected allele frequency of a pathogenic PRSS1 variant (0.000005), strongly supporting that this variant is likely a benign polymorphism. In addition, co-occurrence of this variant and a pathogenic PRSS1 variant (c.365_366delGCinsAT/p.Arg122His) was observed in one patient with chronic pancreatitis (Rygiel_2015). An internal sample with this variant also carries a pathogenic variant (5T_TG12) in CFTR gene. Taken together, this variant is classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000999875 SCV000884413 likely benign not specified 2019-06-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV000149415 SCV001183031 likely benign Hereditary pancreatitis 2018-09-21 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
Forschungslabor Klinik Innere Medizin A University Medicine Greifswald RCV000149415 SCV000196056 unknown Hereditary pancreatitis no assertion criteria provided not provided Converted during submission to Uncertain significance.

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