ClinVar Miner

Submissions for variant NM_000492.3(CFTR):c.1679G>A (p.Arg560Lys) (rs80055610)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CFTR2 RCV000007576 SCV000071523 pathogenic Cystic fibrosis 2017-03-17 reviewed by expert panel research
Integrated Genetics/Laboratory Corporation of America RCV000007576 SCV000696864 pathogenic Cystic fibrosis 2017-06-13 criteria provided, single submitter clinical testing Variant summary: The CFTR c.1679G>A (p.Arg560Lys) variant involves the alteration of a conserved nucleotide at the end of exon 12 and is located in P-loop containing nucleoside triphosphate hydrolase, AAA+ ATPase and/or ABC transporter 1 domain of the protein (InterPro). 4/5 in silico tools predict damaging outcome for this variant. In addition, 5/5 splice prediction tools predict that this variant weakens the canonical 5' splice donor site. This variant has been reported in several CF patients, majority of patients characterized to be pancreatic insufficient (Ferec_1992, Osika_1999, Scotet_2003, Sosnay_2013) and is absent in 118816 control chromosomes from ExAC. Functional analysis shows that this variant leads to defective chloride channel and/or CFTR processing (Sosnay_2013). Multiple clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Other missense changes at the same residue, namely p.Arg560Gly, p.Arg560Ser, and p.Arg560Thr have been reported to associate with CF, indicating Arg560 is a mutational hot-spot. Taken together, this variant is classified as pathogenic.
Counsyl RCV000007576 SCV000799371 likely pathogenic Cystic fibrosis 2018-04-16 criteria provided, single submitter clinical testing
OMIM RCV000007576 SCV000027777 pathogenic Cystic fibrosis 1992-06-01 no assertion criteria provided literature only

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