ClinVar Miner

Submissions for variant NM_004168.4(SDHA):c.1334C>T (p.Ser445Leu)

dbSNP: rs1296066077
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000559654 SCV000651372 likely pathogenic Mitochondrial complex II deficiency, nuclear type 1; Paragangliomas 5 2024-11-19 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 445 of the SDHA protein (p.Ser445Leu). This variant is present in population databases (no rsID available, gnomAD 0.003%). This missense change has been observed in individuals with gastrointestinal stromal tumor, paraganglioma, and/or pheochromocytoma (PMID: 28384794, 29527294, 30854332; internal data). ClinVar contains an entry for this variant (Variation ID: 472322). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SDHA protein function. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Ambry Genetics RCV001011108 SCV001171391 likely pathogenic Hereditary cancer-predisposing syndrome 2024-08-23 criteria provided, single submitter clinical testing The p.S445L variant (also known as c.1334C>T), located in coding exon 10 of the SDHA gene, results from a C to T substitution at nucleotide position 1334. The serine at codon 445 is replaced by leucine, an amino acid with dissimilar properties. This variant has been reported in the germline of multiple patients with SDHA-related paraganglioma-pheochromocytoma syndrome (Currás-Freixes M et al. J Mol Diagn. 2017 07;19:575-588; Bausch B et al. JAMA Oncol. 2017 Sep;3:1204-1212; Bernardo-Castiñeira C et al. Head Neck. 2019 Jan;41:79-91; Díaz-Castellanos MA et al. F1000Res, 2017 Dec;6:2087; Ma X et al. Front Endocrinol (Lausanne), 2020 Dec;11:574662). Based on internal structural analysis, S445L decreases the structure stability (Inaoka DK et al. Int J Mol Sci 2015 Jul;16(7):15287-308). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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 majority of available evidence to date, this variant is likely to be pathogenic.
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV003237919 SCV002009966 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
Baylor Genetics RCV003476307 SCV004200618 uncertain significance Dilated cardiomyopathy 1GG 2023-07-20 criteria provided, single submitter clinical testing
Clinical Genetics Laboratory, Skane University Hospital Lund RCV005231062 SCV005880128 uncertain significance Paraganglioma 2025-03-06 criteria provided, single submitter clinical testing PS3_Supporting, PS4_Moderate, PP3

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