The SDHD gene homepage

Leiden University Medical Center SDHD gene variant database
General information
Gene symbol SDHD
Gene name succinate dehydrogenase complex, subunit D, integral membrane protein
Chromosome 11
Chromosomal band q23
Imprinted Not imprinted
Genomic reference NG_012337.3
Transcript reference NM_003002.2
Exon/intron information NM_003002.2 exon/intron table
Associated with diseases CWS3, PGL1, pheochromocytoma, mitochondrial respiratory chain complex II deficiency, paraganglioma, gastric stromal sarcoma, tumor, carcinoid, intestinal
Citation reference(s) -
Refseq URL Genomic reference sequence
Curators (2) Jean-Pierre Bayley and Peter Taschner
Total number of public variants reported 466
Unique public DNA variants reported 183
Individuals with public variants 555
Hidden variants 2
Download all this gene's data Download all data
Notes Using Mutalyzer? (
Make sure to use this gene-transcript configuration: NG_012337.3(NM_003002.4):

Interpreting In Silico scores in SDH Variant DBs
We provide REVEL (unfortunately, due to technical reasons in the column named "Mutation Taster"), AGVGD and SIFT scores. REVEL (rare exome variant ensemble learner) is an ensemble method for predicting the pathogenicity of missense variants on the basis of the individual tools MutPred, FATHMM, VEST, Poly-Phen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and phastCons. (N.M. Ioannidis et al. American Journal of Human Genetics 99, 877–885, October 6, 2016). Align-GVGD assesses biophysical characteristics of amino acids and protein multiple sequence alignments to predict impact, with a score somewhere between 0 and 250, the higher the scores the more deleterious the change. The GD score is provided and is often very similar to raw Grantham traditional scores. SIFT (Sorting Intolerant From Tolerant) predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. In general, SIFT provides the least informative of the three scores. In general, scores above 0.6 in REVEL and scores above 80 in AGVGD indicate potentially pathogenic variants. Known pathogenic variants present in SDH LOVD invariably show high scores.

In the opinion of the curator the use of the term “VUS” is now excessive. In the case of rare diseases with variants in known causative genes, the emphasis should not be conservative (as in common conditions) but should assume causation and seek supportive evidence (conservation, protein region affected, in silico prediction tools, number of time reported in patients and in gnomAD). Only when no supporting evidence is found should one use the term “VUS”.

CITATION: if you benefit from the use of this database and publish findings, please cite; Bayley JP, Devilee P, Taschner PE (2005). BMC Med Genet. 6:39.

The variants included in the database were derived from the published literature or submitted directly and, where necessary, annotated to conform to current HGVS mutation nomenclature. When you notice any omissions or mistakes, please let us know (thank you).

Disclaimer: inclusion of sequence variants in the SDH mutation database does not imply that there is convincing evidence for pathogenicity.
Date created January 05, 2005
Date last updated May 03, 2023
Version SDHD:230503

Graphical displays and utilities
Graphs Graphs displaying summary information of all variants in the database »
Reading frame checker The Reading-frame checker generates a prediction of the effect of whole-exon changes. Active for: NM_003002.2.
UCSC Genome Browser Show variants in the UCSC Genome Browser (full view, compact view)
Ensembl Genome Browser Show variants in the Ensembl Genome Browser (full view, compact view)
NCBI Sequence Viewer Show distribution histogram of variants in the NCBI Sequence Viewer

Links to other resources
Homepage URL
External URL
HGNC 10683
Entrez Gene 6392
PubMed articles SDHD
OMIM - Gene 602690
OMIM - Diseases CWS3 (Cowden syndrome, type 3 (CWS-3))
PGL1 (paragangliomas, type 1 (PGL-1))
mitochondrial respiratory chain complex II deficiency
paraganglioma, gastric stromal sarcoma
tumor, carcinoid, intestinal
GeneCards SDHD
GeneTests SDHD
Orphanet SDHD

Active transcripts




NCBI ID     

NCBI Protein ID     

00018578 11 succinate dehydrogenase complex, subunit D, integral membrane protein NM_003002.2 NP_002993.1 466

Copyright & disclaimer
The contents of this LOVD database are the intellectual property of the respective submitter(s) and curator(s) of the individual records. Individual data entries may indicate which data license applies to that specific record. When no license is listed, no permissions are granted. Any unauthorized use, copying, storage, or distribution of this material without written permission from the curator(s) will lead to copyright infringement with possible ensuing litigation. Copyright © 2005-2023. All Rights Reserved. For further details, refer to Directive 96/9/EC of the European Parliament and the Council of March 11 (1996) on the legal protection of databases.

We have used all reasonable efforts to ensure that the information displayed on these pages and contained in the databases is of high quality. We make no warranty, express or implied, as to its accuracy or that the information is fit for a particular purpose, and will not be held responsible for any consequences arising from any inaccuracies or omissions. Individuals, organizations, and companies that use this database do so on the understanding that no liability whatsoever, either direct or indirect, shall rest upon the data submitter(s), curator(s), or any of their employees or agents for the effects of any product, process, or method that may be produced or adopted by any part, notwithstanding that the formulation of such product, process or method may be based upon information here provided.