Total submissions: 12
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Counsyl | RCV000006798 | SCV000220653 | likely pathogenic | Renal carnitine transport defect | 2014-08-28 | criteria provided, single submitter | literature only | |
Gene |
RCV000186150 | SCV000239176 | pathogenic | not provided | 2020-10-01 | criteria provided, single submitter | clinical testing | 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: 21922592, 26828774, 28841266, 20027113, 20574985, 21126579, 28711408) |
Invitae | RCV000006798 | SCV000632552 | pathogenic | Renal carnitine transport defect | 2023-12-27 | criteria provided, single submitter | clinical testing | This sequence change replaces glycine, which is neutral and non-polar, with tryptophan, which is neutral and slightly polar, at codon 15 of the SLC22A5 protein (p.Gly15Trp). This variant is present in population databases (rs267607052, gnomAD 0.08%). This missense change has been observed in individual(s) with primary carnitine deficiency (PMID: 20027113, 20574985, 21922592). ClinVar contains an entry for this variant (Variation ID: 6429). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SLC22A5 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects SLC22A5 function (PMID: 21922592). For these reasons, this variant has been classified as Pathogenic. |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000006798 | SCV000698150 | pathogenic | Renal carnitine transport defect | 2017-01-06 | criteria provided, single submitter | clinical testing | Variant summary: The SLC22A5 c.43G>T (p.Gly15Trp) variant involves the alteration of a conserved nucleotide. 4/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 12/116676 control chromosomes at a frequency of 0.0001028, which does not exceed the estimated maximal expected allele frequency of a pathogenic SLC22A5 variant (0.0045644). This variant has been reported in many patients both as homozygotes and compound heterozygote. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic/likely pathogenic. Taken together, this variant is classified as pathogenic. |
Genome- |
RCV000006798 | SCV001821587 | pathogenic | Renal carnitine transport defect | 2021-07-22 | criteria provided, single submitter | clinical testing | |
Revvity Omics, |
RCV000006798 | SCV002020643 | pathogenic | Renal carnitine transport defect | 2022-10-18 | criteria provided, single submitter | clinical testing | |
Giacomini Lab, |
RCV000006798 | SCV002576650 | pathogenic | Renal carnitine transport defect | 2022-10-03 | criteria provided, single submitter | research | |
Fulgent Genetics, |
RCV000006798 | SCV002792002 | likely pathogenic | Renal carnitine transport defect | 2022-01-14 | criteria provided, single submitter | clinical testing | |
Neuberg Centre For Genomic Medicine, |
RCV000006798 | SCV004048048 | likely pathogenic | Renal carnitine transport defect | criteria provided, single submitter | clinical testing | The missense variant c.43G>T (p.Gly15Trp) in SLC22A5 gene has been reported in many patients both as homozygotes and compound heterozygote (Li FY et.al.,2010). Experimental studies have shown that this missense change affects SLC22A5 function (Rose EC et.al.,2012). This variant has been reported to the ClinVar database as Pathogenic/Likely Pathogenic. The p.Gly15Trp variant is reported with allele frequency of 0.009% in gnomAD exomes and novel in 1000 Genomes. The amino acid Gly at position 15 is changed to a Trp changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Likely Pathogenic. In the absence of another reportable variant the molecular diagnosis is not confirmed. | |
Baylor Genetics | RCV000006798 | SCV004201275 | pathogenic | Renal carnitine transport defect | 2024-03-07 | criteria provided, single submitter | clinical testing | |
OMIM | RCV000006798 | SCV000026994 | pathogenic | Renal carnitine transport defect | 2010-01-01 | no assertion criteria provided | literature only | |
Natera, |
RCV000006798 | SCV001458678 | pathogenic | Renal carnitine transport defect | 2020-09-16 | no assertion criteria provided | clinical testing |