ClinVar Miner

Submissions for variant NM_001159773.2(CANT1):c.896C>T (p.Pro299Leu)

gnomAD frequency: 0.00001  dbSNP: rs267606700
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV003398396 SCV004106085 likely pathogenic CANT1-related disorder 2023-10-09 criteria provided, single submitter clinical testing The CANT1 c.896C>T variant is predicted to result in the amino acid substitution p.Pro299Leu. This variant along with a second variant in this gene was reported in two children in one in family with Desbuquois dysplasia (Huber et al. 2009. PubMed ID: 19853239) and found in the homozygous condition in another individual with Desbuquois dysplasia (Biji et al. 2023. PubMed ID: 36331722). This variant is reported in 0.0057% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-76989942-G-A). This variant is interpreted as likely pathogenic.
OMIM RCV000000307 SCV000020451 pathogenic Desbuquois dysplasia 1 2009-11-01 no assertion criteria provided literature only
Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital RCV000000307 SCV002072474 pathogenic Desbuquois dysplasia 1 2022-01-30 no assertion criteria provided clinical testing The homozygous mis-sense variant c.896C>T (p.P299L) has been previously reported by Huber C et al in 2009 as a heterozygous variant in a Brazilian patient. The allele frequency is 0.0004% in gnomAD (aggregated) database. In-silico bioinformatic software predict this variant by mutation taster as Disease causing and SIFT & PROVEAN as Damaging. The phenotype observed was mesomelic shortening of limbs, cystic hygroma, hypoplastic pulmonary artery, hypoplastic lungs, cleft palate, renal cysts, non-immune fetal hydrops. Desbuquois Dysplasia 1 is an autosomal recessive disorder. Based on the phenotypic observation, we classify this variant as likely pathogenic.

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