ClinVar Miner

Submissions for variant NM_001440.4(EXTL3):c.953C>T (p.Pro318Leu)

gnomAD frequency: 0.00003  dbSNP: rs749621890
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV000761559 SCV000891125 likely pathogenic Immunoskeletal dysplasia with neurodevelopmental abnormalities 2019-03-13 criteria provided, single submitter clinical testing The observed variant NM_001440.3:c.953C>T/p.Pro318Leu is a homozygous missense variation in exon 3 of the EXTL3 gene. It has not been reported in the 1000 Genomes and ExAC databases but has been reported as a pathogenic variant by Guo. et al (2017). The in silico prediction of this variant is disease causing by PolyPhen-2, SIFT, LRT and MutationTaster2. The reference codon is conserved across species.
GeneDx RCV001592949 SCV001815202 pathogenic not provided 2019-03-25 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect with significantly decreased enzyme activity compared to wild type (Guo et al., 2017); Not observed at a significant frequency in large population cohorts (Lek et al., 2016; McVean et al., 2012; Exome Variant Server); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 28331220)

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