Download Supplemental Table 2: Candidate gene criteria case example Gene

Supplemental Table 2: Candidate gene criteria case example
Gene
DNM1
Disease
Epileptic encephalopathy
Alteration details
The de novo DNM1 c.1190G>A (p.G397D) alteration is located in the middle domain of the dynamin protein which is involved in self-assembly of dynamin
molecules into dimers and further into tetramers (reviewed in1). In support of pathogenicity, the alteration was not observed in 5,837 individuals studied in
NHLBI Exome Sequencing Project (ESP), and was not observed in the ExAC database. The glycine at this position is highly conserved through evolution and an
alteration to aspartic acid is predicted to be highly deleterious to protein function by multiple in silico methods.2,3 Additional evidence for the deleterious
effect of this alteration came from functional studies of mutant rat dynamin containing the orthologous G397D alteration which was reported to be deficient
in assembly-dependent GTP hydrolysis.4
Alteration
classification
Likely pathogenic (VLP)
Candidate gene
evidence criteria
categories
achieved
Candidate gene
criteria score
Subsequent
details
S-B1
Protein co-localizes or physically interacts with the products of genes implicated in the proposed gene-disease relationship: X-linked loss-of-function
mutations in the SYN1 gene, encoding the synapsin 1 protein, have been identified in patients with epilepsy.5 Similar to dynamin, the synapsin 1 protein has
been shown to be enriched at neuronal synapses and implicated in synaptic vesicle recycling. 6 Heterozygous mutations in another gene, STXBP1 that encodes
the syntaxin 1 binding protein involved in pre-synaptic vesicle docking and fusion for neurotransmitter release, have been shown to be a cause of early
infantile epileptic encephalopathy indicating that perturbations in the neuronal synaptic vesicle recycling pathway, although compatible with life, enhance
susceptibility to the development of seizures in humans.7
S-B2
in vivo model organism with consistent genotype produces phenotype strongly supportive of the proposed gene-disease relationship: A review of animal
models with alterations in the DNM1 gene revealed the existence of the “fitful” mouse that exhibits recurrent limbic and generalized tonic-clonic seizures due
to a heterozygous dominant negative missense alteration, Ala408Thr, located in the middle domain of the dynamin protein and found to be defective in
assembly-dependent endocytosis.8
S-B3
Expression profile is strongly supportive of the proposed gene-disease relationship: Dynamin 1 is expressed predominantly in the brain at pre-synaptic
termini and involved in receptor-mediated endocytosis at neuronal synapses.1,9,10
S-C1
Gene function and/or expression profile is consistent with the phenotype: The DNM1 gene encodes the dynamin 1 protein, a neuron-specific GTPase which
is essential for synaptic vesicle endocytosis during neuronal transmission.1 The role of dynamin in endocytosis was described following studies on the
Drosophila temperature sensitive shibire defects caused by mutations in the Drosophila dynamin gene.11,12 At the non-permissive temperature, these mutant
flies showed rapid paralysis due to depletion of synaptic vesicles as a consequence of blocked clathrin-mediated endocytosis.
S-C3
Gene disruption experiment produces phenotype supportive of the proposed gene-disease relationship: Functional studies of mutant rat dynamin
containing the orthologous G397D alteration was reported to be deficient in assembly-dependent GTP hydrolysis and exerting a dominant negative effect on
the function of the wild type protein by inhibiting endocytosis and normal synaptic vesicular function.4
Candidate
Reclassified to a characterized gene based on strong subsequent corroborating peer-reviewed literature.
1
REFERENCES
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Ferguson SM, De Camilli P. Dynamin, a membrane-remodelling GTPase. Nature reviews. Molecular cell biology.
Feb 2012;13(2):75-88.
Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat
Methods. Apr 2010;7(4):248-249.
Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome research. May 2001;11(5):863-874.
Ford MG, Jenni S, Nunnari J. The crystal structure of dynamin. Nature. Sep 29 2011;477(7366):561-566.
Fassio A, Patry L, Congia S, et al. SYN1 loss-of-function mutations in autism and partial epilepsy cause impaired
synaptic function. Human molecular genetics. Jun 15 2011;20(12):2297-2307.
Greengard P, Valtorta F, Czernik AJ, Benfenati F. Synaptic vesicle phosphoproteins and regulation of synaptic
function. Science. Feb 5 1993;259(5096):780-785.
Saitsu H, Kato M, Mizuguchi T, et al. De novo mutations in the gene encoding STXBP1 (MUNC18-1) cause early
infantile epileptic encephalopathy. Nature genetics. Jun 2008;40(6):782-788.
Boumil RM, Letts VA, Roberts MC, et al. A missense mutation in a highly conserved alternate exon of dynamin-1
causes epilepsy in fitful mice. PLoS genetics. Aug 2010;6(8).
Nakata T, Iwamoto A, Noda Y, Takemura R, Yoshikura H, Hirokawa N. Predominant and developmentally regulated
expression of dynamin in neurons. Neuron. Sep 1991;7(3):461-469.
Cao H, Garcia F, McNiven MA. Differential distribution of dynamin isoforms in mammalian cells. Molecular
biology of the cell. Sep 1998;9(9):2595-2609.
Chen MS, Obar RA, Schroeder CC, et al. Multiple forms of dynamin are encoded by shibire, a Drosophila gene
involved in endocytosis. Nature. Jun 13 1991;351(6327):583-586.
van der Bliek AM, Meyerowitz EM. Dynamin-like protein encoded by the Drosophila shibire gene associated with
vesicular traffic. Nature. May 30 1991;351(6325):411-414.
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