ClinVar Miner

Submissions for variant NM_003000.3(SDHB):c.688C>T (p.Arg230Cys)

gnomAD frequency: 0.00001  dbSNP: rs138996609
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000164435 SCV000215074 pathogenic Hereditary cancer-predisposing syndrome 2022-11-22 criteria provided, single submitter clinical testing The p.R230C pathogenic mutation (also known as c.688C>T), located in coding exon 7 of the SDHB gene, results from a C to T substitution at nucleotide position 688. The arginine at codon 230 is replaced by cysteine, an amino acid with highly dissimilar properties. This pathogenic variant has been reported in numerous individuals diagnosed with pheochromocytomas and/or paragangliomas (Gimenez-Roqueplo AP et al. Cancer Res. 2003 Sep 1;63(17):5615-21; Dahia PL et al. PLoS Genet. 2005 Jul;1(1):72-80; Neumann HP et al. Cancer Res. 2009 Apr 15;69(8):3650-6; Sevilla MA et al. Otolaryngol Head Neck Surg. 2009 May;140(5):724-9; Burnichon N et al. J Clin Endocrinol Metab. 2009 Aug;94(8):2817-27; Yang C et al. FASEB J. 2012 Nov;26(11):4506-16; Andrews KA et al. J. Med. Genet. 2018 Jun;55:384-394). Additionally, two disease-causing variants, p.R230H and p.R230L, have been described in the same codon. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
GeneDx RCV000520697 SCV000617569 pathogenic not provided 2017-10-05 criteria provided, single submitter clinical testing This pathogenic variant is denoted SDHB c.688C>T at the cDNA level, p.Arg230Cys (R230C) at theprotein level, and results in the change of an Arginine to a Cysteine (CGC>TGC). This variant was observed in severalindividuals with pheochromocytoma or paraganglioma (Gimenez-Roqueplo 2003, Lefebvre 2012, Hermsen 2010,Janssen, Jochmanova 2017). In addition, functional assays have demonstrated this variant to result in an unstableprotein, and in the tumor of an individual harboring this variant, complete and selective loss of mitochondrial complex IIenzyme activity was observed (Yang 2012, Gimenez-Roqueplo 2003). SDHB Arg230Cys was not observed at asignificant allele frequency in large population cohorts (Lek 2016). Since Arginine and Cysteine differ in polarity,charge, size or other properties, this is considered a non-conservative amino acid substitution. SDHB Arg230Cysoccurs at a position that is conserved across species and is not located in a known functional domain. In silicoanalyses predict that this pathogenic variant is probably damaging to protein structure and function. Based on currentlyavailable evidence, we consider this variant to be pathogenic
Invitae RCV000528137 SCV000644765 pathogenic Gastrointestinal stromal tumor; Paragangliomas 4; Pheochromocytoma 2023-12-01 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 230 of the SDHB protein (p.Arg230Cys). This variant is present in population databases (rs138996609, gnomAD 0.0009%). This missense change has been observed in individuals with malignant or non-malignant pheochromocytoma or paraganglioma (PMID: 14500403, 17652212, 19454582, 20208144, 22517554, 25873086). ClinVar contains an entry for this variant (Variation ID: 185077). 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 SDHB protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects SDHB function (PMID: 22835832). This variant disrupts the p.Arg230 amino acid residue in SDHB. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 18382370, 19351833, 23934599; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Center for Human Genetics, Inc, Center for Human Genetics, Inc RCV000660258 SCV000782279 pathogenic Paragangliomas 4 2016-11-01 criteria provided, single submitter clinical testing
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine RCV000660258 SCV000840068 pathogenic Paragangliomas 4 2018-01-14 criteria provided, single submitter clinical testing The c.688C>T (p.Arg230Cys) variant in the SDHB gene has been reported in several unrelated individuals with pheochromocytoma or paraganglioma (PMID: 14500403, 24939699, 20208144, and 28374168). Functional assays have demonstrated that this missense change results in an unstable protein, and in the tumor of an individual with this variant complete and selective loss of mitochondrial complex II enzyme activity was observed (PMID: 22835832, 14500403). Additionally, two other pathogenic/likely pathogenic missense substitutions at this codon have been reported (PMID: 22835832, 23934599, 18382370, and 19351833,) suggesting that the Arg230 residue is critical for normal functioning of the SDHB protein. In light of the currently available data this variant in the SDHB gene is classified pathogenic.
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV000660258 SCV001369396 pathogenic Paragangliomas 4 2020-01-06 criteria provided, single submitter clinical testing This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PP3.
Myriad Genetics, Inc. RCV000660258 SCV004017902 likely pathogenic Paragangliomas 4 2023-02-08 criteria provided, single submitter clinical testing This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 14500403, 33362715, 28374168, 34906457]. This variant is expected to disrupt protein structure [Myriad internal data].
All of Us Research Program, National Institutes of Health RCV000505374 SCV004821938 pathogenic Hereditary pheochromocytoma-paraganglioma 2023-08-08 criteria provided, single submitter clinical testing This missense variant replaces arginine with cysteine at codon 230 of the SDHB protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant may impact protein stability and increase SDHB ubiquitination (PMID: 14500403, 22835832, 35673401). This variant has been reported in individuals affected with pheochromocytomas, paragangliomas, and gastrointestinal stromal tumors (PMID: 16103922, 17652212, 19351833, 19454582, 20208144, 22517554, 25873086, 29386252, 30536464, 34906457, 33420946, 35673401, 35904169). Other amino acid changes at this codon are considered disease causing (R230L, R230H, R230G; ClinVar Variant IDs: 184933, 142637, 1755980). This variant has been identified in 2/251398 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
Section on Medical Neuroendocrinolgy, National Institutes of Health RCV000505374 SCV000599523 pathogenic Hereditary pheochromocytoma-paraganglioma no assertion criteria provided research

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