ClinVar Miner

Submissions for variant NM_021942.6(TRAPPC11):c.2938G>A (p.Gly980Arg)

gnomAD frequency: 0.00001  dbSNP: rs397509417
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000054408 SCV000807243 pathogenic Autosomal recessive limb-girdle muscular dystrophy type R18 2017-09-01 criteria provided, single submitter clinical testing This variant has been previously reported as disease-causing and was found once in our laboratory homozygous in a 1-year-old female with motor delays, hypotonia, elevated CK and transaminases.
Labcorp Genetics (formerly Invitae), Labcorp RCV000054408 SCV000945321 pathogenic Autosomal recessive limb-girdle muscular dystrophy type R18 2023-11-17 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 980 of the TRAPPC11 protein (p.Gly980Arg). This variant is present in population databases (rs397509417, gnomAD 0.08%). This missense change has been observed in individual(s) with TRAPPC11-related conditions (PMID: 23830518, 26322222; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 60510). 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 TRAPPC11 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects TRAPPC11 function (PMID: 23830518, 26912795). For these reasons, this variant has been classified as Pathogenic.
MGZ Medical Genetics Center RCV000054408 SCV002581874 likely pathogenic Autosomal recessive limb-girdle muscular dystrophy type R18 2022-08-29 criteria provided, single submitter clinical testing
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000054408 SCV004801266 pathogenic Autosomal recessive limb-girdle muscular dystrophy type R18 2024-03-14 criteria provided, single submitter research
Juno Genomics, Hangzhou Juno Genomics, Inc RCV000054408 SCV005417132 pathogenic Autosomal recessive limb-girdle muscular dystrophy type R18 criteria provided, single submitter clinical testing PM2_Supporting+PP3+PM3_VeryStrong+PP4
OMIM RCV000054408 SCV000082885 pathogenic Autosomal recessive limb-girdle muscular dystrophy type R18 2013-07-11 no assertion criteria provided literature only

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