Submissions for variant NM_003000.3(SDHB):c.758G>A (p.Cys253Tyr)

dbSNP: rs786201085

Total submissions: 4

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000162580	SCV000212996	likely pathogenic	Hereditary cancer-predisposing syndrome	2018-06-21	criteria provided, single submitter	clinical testing	The p.C253Y variant (also known as c.758G>A) is located in coding exon 7 of the SDHB gene. This alteration results from a G to A substitution at nucleotide position 758. The cysteine at codon 253 is replaced by tyrosine, an amino acid with highly dissimilar properties. Multiple studies have identified this alteration in patients with pheochromocytomas and/or paragangliomas, often with apparently sporadic presentation (Amar L et al. J. Clin Oncol 2005 Dec 1;23(34):8812-8, Amar L et al. J. Clin. Endocrinol. Metab. 2007 Oct; 92(10):3822-8, Favier J et al. PLoS ONE 2009;4(9):e7094, Burnichon N et al. J. Clin. Endocrinol. Metab. 2009 Aug; 94(8):2817-27; Patócs A et al. Pathol. Oncol. Res. 2016 Oct;22(4):673-9). Based on protein sequence alignment, this amino acid position is highly conserved and located in a highly conserved region of the protein. The Cys253 residue plays a vital role coordinating the Fe4S4 cluster, and it is believed that alterations at this location would prevent assembly of Complex II (Iverson TM et al. J. Biol. Chem. 2012 Oct; 287(42):35430-8). In addition, this alteration is predicted to be probably damaging and deleterious by PolyPhen and SIFT in silico analyses, respectively. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001040032	SCV001203587	pathogenic	Gastrointestinal stromal tumor; Paragangliomas 4; Pheochromocytoma	2023-08-04	criteria provided, single submitter	clinical testing	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. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 183795). This missense change has been observed in individuals with paraganglioma-pheochromocytoma syndrome (PMID: 17652212, 19454582, 19763184, 26960314). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 253 of the SDHB protein (p.Cys253Tyr).
Color Diagnostics, LLC DBA Color Health	RCV003514319	SCV004362267	pathogenic	Paragangliomas 4	2023-06-16	criteria provided, single submitter	clinical testing	This missense variant replaces cysteine with tyrosine at codon 253 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 abolished both the succinate co-Q oxidoreductase (SQR) activity and succinate dehydrogenase (SDH) activity of mitochondrial complex II, and impaired SDHB association with SDHA and the formation of the full SDH complex (CII; PMID: 26719882). This variant has been reported in numerous individuals affected with paraganglioma and pheochromocytoma in the literature (PMID: 16314641, 17652212, 19454582, 19763184, 22517557,26960314, 34439371). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
All of Us Research Program, National Institutes of Health	RCV003995206	SCV004825235	pathogenic	Hereditary pheochromocytoma-paraganglioma	2023-08-15	criteria provided, single submitter	clinical testing	This missense variant replaces cysteine with tyrosine at codon 253 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 abolished both the succinate co-Q oxidoreductase (SQR) activity and succinate dehydrogenase (SDH) activity of mitochondrial complex II, and impaired SDHB association with SDHA and the formation of the full SDH complex (CII; PMID: 26719882). This variant has been reported in numerous individuals affected with paraganglioma and pheochromocytoma in the literature (PMID: 16314641, 17652212, 19454582, 19763184, 22517557,26960314, 34439371). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.