Human Gene Module / Chromosome 9 / DNM1

DNM1dynamin 1

SFARI Gene Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
5 / 11
Rare Variants / Common Variants
33 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
9q34.11
Associated Disorders
-
Relevance to Autism

A de novo missense variant in the DNM1 gene was identified in an ASD proband from the SPARK proband (Feliciano et al., 2019), while a damaging missense variant in this gene was identified in three ASD-affected siblings from the BARAKA-Qatar study and their father, who was diagnosed with ADHD and presented with autistic features (Abdi et al., 2023). Additional loss-of-function and damaging missense variants in DNM1 were reported in individuals from ASD and developmental delay cohorts in Wang et al., 2020. One of the five individuals with DNM1-related autosomal dominant developmental and epileptic encephalopathy described in EuroEPINOMICS-RES Consortium 2014 was reported to have autism spectrum disorder, while both individuals with DNM1-related autosomal recessive developmental and epileptic encephalopathy described in Yigit et al., 2022 were reported to present with stereotypical movements. A de novo missense variant in DNM1 was identified in twin siblings presenting with diagnoses of autism spectrum disorder, developmental delay, and intellectual disability without epileptic encephalopathy in Brereton et al., 2018, while a de novo missense variant in this gene was reported in a adult male with autism, intellectual disability, and mild epilepsy in Mei et al., 2023.

Molecular Function

This gene encodes a member of the dynamin subfamily of GTP-binding proteins. The encoded protein possesses unique mechanochemical properties used to tubulate and sever membranes, and is involved in clathrin-mediated endocytosis and other vesicular trafficking processes. Actin and other cytoskeletal proteins act as binding partners for the encoded protein, which can also self-assemble leading to stimulation of GTPase activity. Heterozygous and homozygous mutations in this gene are responsible for autosomal dominant and autosomal recessive forms of developmental and epileptic encephalopathy, respectively (EuroEPINOMICS-RES Consortium 2014; Deciphering Developmental Disorders Study 2015; Yigit et al., 2022; AlTassan et al., 2022).

SFARI Genomic Platforms
Reports related to DNM1 (11 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies EuroEPINOMICS-RES Consortium , et al. (2014) No ASD
2 Support Large-scale discovery of novel genetic causes of developmental disorders Deciphering Developmental Disorders Study (2014) No -
3 Support - Emily Brereton et al. (2018) Yes -
4 Support Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes Feliciano P et al. (2019) Yes -
5 Support Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders Wang T et al. (2020) Yes -
6 Support - Gökhan Yigit et al. (2022) No Stereotypy
7 Support - Ruqaiah AlTassan et al. (2022) No -
8 Support - Davide Mei et al. () Yes -
9 Primary - Mona Abdi et al. (2023) Yes ADHD
10 Support - Purvi Majethia et al. (2024) No DD
11 Support - Axel Schmidt et al. (2024) No -
Rare Variants   (33)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.1335+1701C>T - stop_gained Unknown - - 33004838 Wang T et al. (2020)
c.766C>T p.Arg256Ter stop_gained Familial - - 33004838 Wang T et al. (2020)
c.1261C>T p.Arg421Ter stop_gained Familial - - 33004838 Wang T et al. (2020)
c.1622dup p.Tyr541Ter stop_gained Familial - - 33004838 Wang T et al. (2020)
c.199C>T p.Arg67Cys missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.596G>T p.Arg199Leu missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.709C>T p.Arg237Trp missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.788C>T p.Pro263Leu missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.812G>A p.Arg271His missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.889C>T p.Arg297Trp missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.1037G>A p.Gly346Asp missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.1268C>T p.Pro423Leu missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.1291G>A p.Val431Ile missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.1300G>A p.Glu434Lys missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.1394G>A p.Arg465Gln missense_variant Unknown - - 33004838 Wang T et al. (2020)
c.1994T>C p.Leu665Pro missense_variant De novo - - 37132416 Davide Mei et al. ()
c.1154G>A p.Arg385Gln missense_variant Familial - - 33004838 Wang T et al. (2020)
c.1197-8G>A - splice_region_variant De novo - - 38374498 Purvi Majethia et al. (2024)
c.1660A>G p.Lys554Glu missense_variant De novo - - 31452935 Feliciano P et al. (2019)
c.1180A>G p.Asn394Asp missense_variant De novo - - 39039281 Axel Schmidt et al. (2024)
c.97C>T p.Gln33Ter stop_gained Familial Both parents Simplex 34172529 Gökhan Yigit et al. (2022)
c.796C>T p.Arg266Cys missense_variant Familial Paternal Multiplex 37805537 Mona Abdi et al. (2023)
c.850C>T p.Gln284Ter stop_gained Familial Both parents Simplex 34172529 Gökhan Yigit et al. (2022)
c.194C>A p.Thr65Asn missense_variant De novo - Simplex 25262651 EuroEPINOMICS-RES Consortium , et al. (2014)
c.529G>C p.Ala177Pro missense_variant De novo - Simplex 25262651 EuroEPINOMICS-RES Consortium , et al. (2014)
c.618G>C p.Lys206Asn missense_variant De novo - Simplex 25262651 EuroEPINOMICS-RES Consortium , et al. (2014)
c.709C>T p.Arg237Trp missense_variant De novo - Simplex 25262651 EuroEPINOMICS-RES Consortium , et al. (2014)
c.1076G>C p.Gly359Ala missense_variant De novo - Simplex 25262651 EuroEPINOMICS-RES Consortium , et al. (2014)
c.865A>T p.Ile289Phe missense_variant De novo - Simplex 25533962 Deciphering Developmental Disorders Study (2014)
c.709C>T p.Arg237Trp missense_variant De novo - Unknown 25533962 Deciphering Developmental Disorders Study (2014)
c.1186C>G p.His396Asp missense_variant De novo - Simplex 25533962 Deciphering Developmental Disorders Study (2014)
c.1603A>G p.Lys535Glu missense_variant De novo - Multiplex (monozygotic twins) 29397573 Emily Brereton et al. (2018)
c.350del p.Pro117ArgfsTer14 frameshift_variant Familial Both parents Simplex 36553519 Ruqaiah AlTassan et al. (2022)
Common Variants  

No common variants reported.

SFARI Gene score
3

Suggestive Evidence

Score Delta: Score remained at 3

3

Suggestive Evidence

See all Category 3 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.

1/1/2024
icon
3

Increased from to 3

Krishnan Probability Score

Score 0.56936662424081

Ranking 1038/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
ExAC Score

Score 0.99986383931626

Ranking 726/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score

Score 0.94178402462613

Ranking 15061/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Zhang D Score

Score 0.42618499754193

Ranking 1164/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
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