ClinVar Miner

Submissions for variant NM_006907.4(PYCR1):c.616G>A (p.Gly206Arg)

gnomAD frequency: 0.00002  dbSNP: rs121918375
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000059738 SCV000617790 pathogenic not provided 2022-12-09 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 32949114, 25525159, 19648921, 27023906, 27860360, 22887749, 21487760, 24035636, 29620724, 31829210, 34426522)
Eurofins Ntd Llc (ga) RCV000059738 SCV000709428 likely pathogenic not provided 2017-06-29 criteria provided, single submitter clinical testing
Kariminejad - Najmabadi Pathology & Genetics Center RCV001814045 SCV001755600 pathogenic Abnormality of connective tissue 2021-07-10 criteria provided, single submitter clinical testing
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV004017383 SCV004847216 pathogenic Autosomal recessive cutis laxa type 2B 2023-09-06 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004700370 SCV005205224 pathogenic Cutis laxa 2024-06-14 criteria provided, single submitter clinical testing Variant summary: PYCR1 c.616G>A (p.Gly206Arg) results in a non-conservative amino acid change located in the Pyrroline-5-carboxylate reductase, dimerisation domain (IPR029036) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.1e-05 in 186106 control chromosomes. c.616G>A has been reported in the literature in the homozygous state in multiple individuals affected with Cutis Laxa - PYCR1 Related (example, Dimopoulou_2013, Reversade_2009). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 24035636, 19648921). ClinVar contains an entry for this variant (Variation ID: 68789). Based on the evidence outlined above, the variant was classified as pathogenic.
UniProtKB/Swiss-Prot RCV000059738 SCV000091308 not provided not provided no assertion provided not provided

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