Submissions for variant NM_003002.4(SDHD):c.479G>T (p.Ter160Leu)

gnomAD frequency: 0.00002  dbSNP: rs201372601

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000454533	SCV000540308	uncertain significance	not specified	2016-10-20	criteria provided, single submitter	clinical testing	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Extension variant reported in 1 proband with autosomal recessive encephalomyopathy and MT complex II deficiency - proband carried E69K on other allele. Complementation of a patient cell line supported the pathogenicity of the SDHD variants.
Invitae	RCV002228513	SCV000554058	uncertain significance	Carney-Stratakis syndrome; Pheochromocytoma; Paragangliomas with sensorineural hearing loss; Cowden syndrome 3	2024-01-21	criteria provided, single submitter	clinical testing	This sequence change disrupts the translational stop signal of the SDHD mRNA. It is expected to extend the length of the SDHD protein by 3 additional amino acid residues. This variant is present in population databases (rs201372601, gnomAD 0.0009%). This protein extension has been observed in individual(s) with mitochondrial complex II deficiency (PMID: 24367056). ClinVar contains an entry for this variant (Variation ID: 156154). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this protein extension affects SDHD function (PMID: 24367056). 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000454533	SCV000918203	uncertain significance	not specified	2018-12-04	criteria provided, single submitter	clinical testing	Variant summary: SDHD c.479G>T (p.X160LeuextX3) changes the termination codon and is predicted to lead to an extended protein with additional 3 amino acids added to the normal C-terminus. The variant allele was found at a frequency of 4.1e-06 in 242834 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.479G>T has been reported in the literature in one individual affected with mitochondrial complex II deficiency in compound heterozygous state (Jackson_2014). This report does not provide unequivocal conclusions about association of the variant with Hereditary Paraganglioma-Pheochromocytoma Syndrome. One publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about causality of the variant (Jackson_2014). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Both laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.
CeGaT Center for Human Genetics Tuebingen	RCV000994727	SCV001148462	likely pathogenic	not provided	2019-04-01	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV001023072	SCV001184892	likely pathogenic	Hereditary cancer-predisposing syndrome	2023-05-15	criteria provided, single submitter	clinical testing	The c.479G>T variant (also known as p.*160Lext*3), located in coding exon 4 of the SDHD gene, results from a G to T substitution at nucleotide position 479, which is the second to last nucleotide of the SDHD gene. This alteration disrupts the stop codon of the SDHD gene and is predicted to preserve the native sequence while resulting in the elongation of the protein by 3 amino acids. The exact functional effect of the additional amino acids is unknown. This alteration has been reported as compound heterozygous with a second SDHD alteration, p.E69K, in an individual with autosomal recessive encephalomyopathy and isolated mitochondrial complex II deficiency (Jackson CB et al. J. Med. Genet., 2014 Mar;51:170-5). Functional studies demonstrated that the introduction of this variant to patient cells was unable to recover complex II formation compared to a WT control (Jackson CB et al. J. Med. Genet., 2014 Mar;51:170-5). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the majority of available evidence to date, this variant is likely to be pathogenic in association with mitochondrial complex II deficiency; however, the clinical significance in regards to paraganglioma-pheochromocytoma syndrome remains unclear.
GeneDx	RCV000994727	SCV001780853	likely pathogenic	not provided	2023-08-26	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a damaging effect: reduced enzyme activities of the individual respiratory chains complexes in skeletal muscle and inability to restore the complex II assembly in a fibroblast cell line (Jackson et al., 2014); Normal stop codon changed to a Leucine codon, leading to the addition of 3 amino acids at the C-terminus; Not observed at significant frequency in large population cohorts (gnomAD); Also known as p.X104LextX3; This variant is associated with the following publications: (PMID: 24367056, 34012134, 33162331)
OMIM	RCV000144172	SCV000189249	pathogenic	Mitochondrial complex 2 deficiency, nuclear type 3	2014-03-01	no assertion criteria provided	literature only
Section on Medical Neuroendocrinolgy, National Institutes of Health	RCV000505355	SCV000599548	uncertain significance	Hereditary pheochromocytoma-paraganglioma		no assertion criteria provided	research