rs80338846
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate
The NM_003002.4(SDHD):c.284T>C(p.Leu95Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L95R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_003002.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDHD | NM_003002.4 | c.284T>C | p.Leu95Pro | missense_variant | 3/4 | ENST00000375549.8 | NP_002993.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDHD | ENST00000375549.8 | c.284T>C | p.Leu95Pro | missense_variant | 3/4 | 1 | NM_003002.4 | ENSP00000364699 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 19, 2022 | The p.L95P pathogenic mutation (also known as c.284T>C), located in coding exon 3 of the SDHD gene, results from a T to C substitution at nucleotide position 284. The leucine at codon 95 is replaced by proline, an amino acid with similar properties. This alteration has been described as a Dutch founder mutation and has been identified in multiple patients and families with paragangliomas/pheochromocytomas, and was shown to segregate with disease in at least two families (Taschner PE et al. Genes Chromosomes Cancer, 2001 Jul;31:274-81; Cremers CW et al. Otol. Neurotol., 2002 Sep;23:755-9; Hensen EF et al. Clin. Genet., 2012 Mar;81:284-8; van Hulsteijn LT et al. Clin. Endocrinol. (Oxf), 2013 Dec;79:824-31; Bayley JP et al. BMC Med. Genet., 2014 Oct;15:111; Heesterman BL et al. Eur J Hum Genet, 2018 09;26:1339-1347; Richter S et al. Genet Med, 2019 03;21:705-717; Dreijerink KMA et al. J Clin Endocrinol Metab, 2019 11;104:5421-5426). 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. - |
Hereditary pheochromocytoma-paraganglioma Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at