Submissions for variant NM_001039141.3(TRIOBP):c.7010G>A (p.Arg2337Gln)

gnomAD frequency: 0.00004  dbSNP: rs200850285

Total submissions: 4

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000604907	SCV000712185	likely benign	not specified	2016-06-02	criteria provided, single submitter	clinical testing	p.Arg2337Gln in exon 23 of TRIOBP: This variant is not expected to have clinical significance due to a lack of conservation across species, including mammals. O f note, 6 mammals have a Glutamine (Gln) at this position despite high nearby am ino acid conservation. It has been identified in 6/66534 of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSN P rs200850285).
GeneDx	RCV001358179	SCV002513722	uncertain significance	not provided	2022-05-10	criteria provided, single submitter	clinical testing	In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Invitae	RCV001358179	SCV003286916	uncertain significance	not provided	2022-02-18	criteria provided, single submitter	clinical testing	ClinVar contains an entry for this variant (Variation ID: 505078). This variant has not been reported in the literature in individuals affected with TRIOBP-related conditions. This variant is present in population databases (rs200850285, gnomAD 0.2%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 2337 of the TRIOBP protein (p.Arg2337Gln). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001358179	SCV001553850	uncertain significance	not provided		no assertion criteria provided	clinical testing	The TRIOBP p.Arg624Gln variant was identified in dbSNP (ID: rs200850285), ClinVar (classified as likely benign by Laboratory for Molecular Medicine) and LOVD 3.0 (classified as a VUS) but was not identified in the literature. The variant was identified in control databases in 27 of 249472 chromosomes at a frequency of 0.000108 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Ashkenazi Jewish in 21 of 10070 chromosomes (freq: 0.002085), Other in 2 of 6066 chromosomes (freq: 0.00033), South Asian in 1 of 30600 chromosomes (freq: 0.000033), Latino in 1 of 34520 chromosomes (freq: 0.000029) and European (non-Finnish) in 2 of 113246 chromosomes (freq: 0.000018), but was not observed in the African, East Asian, or European (Finnish) populations. The p.Arg624 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.