Submissions for variant NM_000531.6(OTC):c.674C>T (p.Pro225Leu)

dbSNP: rs67120076

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000083536	SCV000330994	pathogenic	not provided	2015-11-03	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000011747	SCV000825697	pathogenic	Ornithine carbamoyltransferase deficiency	2024-10-07	criteria provided, single submitter	clinical testing	This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 225 of the OTC protein (p.Pro225Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with ornithine transcarbamylase (OTC) deficiency (PMID: 1721894, 9286441, 9427144, 27070778). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 11000). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt OTC protein function with a positive predictive value of 95%. This variant disrupts the p.Pro225 amino acid residue in OTC. Other variant(s) that disrupt this residue have been observed in individuals with OTC-related conditions (PMID: 9427144, 10946359, 19669271), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000011747	SCV001364018	pathogenic	Ornithine carbamoyltransferase deficiency	2019-08-29	criteria provided, single submitter	clinical testing	Variant summary: OTC c.674C>T (p.Pro225Leu) results in a non-conservative amino acid change located in the Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain (IPR006131) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 182904 control chromosomes (gnomAD). The variant, c.674C>T, has been reported in the literature in multiple individuals affected with Ornithine Transcarbamylase Deficiency (OTCD) (Hentzen_1991, Garcia-Perez_1997, Matsuda_1997, McCullough_2000, Bijarnia-Mahay_2018). Hentzen_1991 reported this variant to segregate with OTCD in one family. These data indicate that the variant is very likely to be associated with disease. Several publications also reported (near) undetectable residual enzyme activities from patient samples (Hentzen_1991, Garcia-Perez_1997, Matsuda_1997, McCullough_2000). Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely pathogenic (1x) or pathogenic (2x). Based on the evidence outlined above, the variant was classified as pathogenic.
Genome-Nilou Lab	RCV000011747	SCV002033227	pathogenic	Ornithine carbamoyltransferase deficiency	2021-11-07	criteria provided, single submitter	clinical testing
OMIM	RCV000011747	SCV000031979	pathogenic	Ornithine carbamoyltransferase deficiency	1991-12-01	no assertion criteria provided	literature only
GenMed Metabolism Lab	RCV000083536	SCV000115622	pathogenic	not provided		no assertion criteria provided	not provided	Converted during submission to Pathogenic.
Genomic Research Center, Shahid Beheshti University of Medical Sciences	RCV000011747	SCV000268692	likely pathogenic	Ornithine carbamoyltransferase deficiency	2016-05-09	no assertion criteria provided	clinical testing