rs202198133
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_003002.4(SDHD):c.205G>A(p.Glu69Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,460,472 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. E69E) has been classified as Likely benign.
Frequency
Consequence
NM_003002.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDHD | NM_003002.4 | c.205G>A | p.Glu69Lys | missense_variant | 3/4 | ENST00000375549.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDHD | ENST00000375549.8 | c.205G>A | p.Glu69Lys | missense_variant | 3/4 | 1 | NM_003002.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251256Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135792
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1460472Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726538
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Mitochondrial complex II deficiency, nuclear type 1 Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Rare Disease Group, University of Exeter | Jul 23, 2020 | - - |
Pheochromocytoma;C1847319:Carney-Stratakis syndrome;C1868633:Paragangliomas with sensorineural hearing loss;CN166604:Cowden syndrome 3 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 69 of the SDHD protein (p.Glu69Lys). This variant is present in population databases (rs202198133, gnomAD 0.002%). This missense change has been observed in individual(s) with clinical features of autosomal recessive mitochondrial complex II deficiency (PMID: 24367056, 34012134). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 156153). 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) has been performed at Invitae 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 SDHD protein function. Experimental studies have shown that this missense change affects SDHD function (PMID: 24367056). For these reasons, this variant has been classified as Pathogenic. - |
Mitochondrial complex 2 deficiency, nuclear type 3 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2014 | - - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 05, 2022 | Not observed at significant frequency in large population cohorts (gnomAD); 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); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29504908, 33162331, 34012134, 24367056) - |
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2024 | The p.E69K variant (also known as c.205G>A), located in coding exon 3 of the SDHD gene, results from a G to A substitution at nucleotide position 205. The glutamic acid at codon 69 is replaced by lysine, an amino acid with similar properties. This alteration has been reported in the compound heterozygous state with a second SDHD alteration 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). This alteration was also observed to be homozygous in several members of one family who were determined to have mitochondrial complex II deficiency (Lin S et al. Eur J Hum Genet 2021 10;29(10):1570-1576). 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 expected to be causative of autosomal recessive mitochondrial complex II deficiency when present along with a second likely pathogenic/pathogenic variant on the other allele; however, its clinical significance for autosomal dominant paraganglioma-pheochromocytoma syndrome is unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at