ClinVar Miner

Submissions for variant NM_003122.4(SPINK1):c.1A>T (p.Met1Leu) (rs369163833)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Integrated Genetics/Laboratory Corporation of America RCV000590221 SCV000698173 uncertain significance not provided 2017-07-31 criteria provided, single submitter clinical testing Variant summary: The SPINK1 c.1A>T (p.Met1Leu) variant involves the alteration of a conserved nucleotide and the start codon. There is no second Met in SPINK1 protein, suggesting the abolishment of the Met1 is likely to be damaging. In consistency with this prediction, 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant is absent in 119498 control chromosomes and has been reported in at least one patient with chronic pancreatitis with co-occurrence of a pathogenic variant SPINK1 p.Asn34Ser (Masson_2008). Another start codon loss, p.Met1Thr, has been reported to associate with chronic pancreatitis (HGMD database). Taken together, this variant is classified as VUS-possibly pathogenic until more information becomes available.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000590221 SCV000884573 pathogenic not provided 2017-07-03 criteria provided, single submitter clinical testing
Mendelics RCV000987609 SCV001136992 likely pathogenic Hereditary pancreatitis 2019-05-28 criteria provided, single submitter clinical testing

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