DNM1 dynamin 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DNM1provided by HGNC
Official Full Name: dynamin 1provided by HGNC
Primary source: HGNC:HGNC:2972
See related: Ensembl:ENSG00000106976 MIM:602377; AllianceGenome:HGNC:2972
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DNM; DEE31; DEE31A; DEE31B; EIEE31
Summary: 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. More than sixty highly conserved copies of the 3' region of this gene are found elsewhere in the genome, particularly on chromosomes Y and 15. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Expression: Biased expression in brain (RPKM 103.8) and gall bladder (RPKM 8.7) See more
Orthologs: mouse all
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Genomic context

Location:: 9q34.11

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (128203379..128255244)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (140410459..140462358)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (130965658..131017523)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism.
Title: A recurrent de novo splice site variant involving DNM1 exon 10a causes developmental and epileptic encephalopathy through a dominant-negative mechanism.
Loss-of-function variants in DNM1 cause a specific form of developmental and epileptic encephalopathy only in biallelic state.
Title: Loss-of-function variants in DNM1 cause a specific form of developmental and epileptic encephalopathy only in biallelic state.
Dynamin regulates L cell secretion in human gut.
Title: Dynamin regulates L cell secretion in human gut.
CryoEM structure of the super-constricted two-start dynamin 1 filament.
Title: CryoEM structure of the super-constricted two-start dynamin 1 filament.
3.75 A resolution cryo-electron microscopy structure of the membrane-associated helical polymer of human dynamin-1 in the GMPPCP-bound state
Title: Cryo-EM of the dynamin polymer assembled on lipid membrane.
Cellular fluorescein hyperfluorescence is dynamin-dependent.
Title: Cellular fluorescein hyperfluorescence is dynamin-dependent and increased by Tetronic 1107 treatment.
The twin siblings exhibit mild to moderate intellectual disability and autistic symptoms but no epileptic encephalopathy. Exome sequencing revealed a genetic variant, c.1603A>G (p.Lys535Glu), in the PH domain of dynamin 1. The twin sisters studied here share the de novo variant, c.1603A>G (p.Lys535Glu) in exon 15 of DNM1, classified as likely pathogenic.
Title: Mutations in the PH Domain of DNM1 are associated with a nonepileptic phenotype characterized by developmental delay and neurobehavioral abnormalities.
The data show that the dynamin-amphiphysin helices are rearranged to form clusters upon GTP hydrolysis and membrane constriction occurs at protein-uncoated regions flanking the clusters.
Title: Dynamic clustering of dynamin-amphiphysin helices regulates membrane constriction and fission coupled with GTP hydrolysis.
Together, these observations suggest that while endophilin helps shape endocytic tubules and recruit dynamin to endocytic sites, it can also block membrane fission when present in excess by inhibiting inter-dynamin interactions.
Title: Structural inhibition of dynamin-mediated membrane fission by endophilin.
The authors show that in fibroblasts, dynamin GTP hydrolysis occurs as stochastic bursts, which are randomly distributed relatively to the peak of dynamin assembly. Thus, dynamin disassembly is not coupled to GTPase activity, supporting that the GTP energy is primarily spent in constriction.
Title: Uncoupling of dynamin polymerization and GTPase activity revealed by the conformation-specific nanobody dynab.

Submit: New GeneRIF Correction See all GeneRIFs (65)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Developmental and epileptic encephalopathy, 31A MedGen: C4225357 OMIM: 616346 GeneReviews: Not available	not available
Developmental and epileptic encephalopathy, 31B MedGen: C5830459 OMIM: 620352 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Dynamin-dependent endocytosis is required for intracellular accumulation of HIV-1 Gag in the presence of HLA-DR	PubMed
	gag	HIV-1 Gag co-localizes with dynamin in primary T lymphocytes	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH80788 (e-PCR)
- UniSTS:86551

RH79965 (e-PCR)
- UniSTS:83820

D10S16 (e-PCR)
- UniSTS:155756

D15S1477 (e-PCR)
- UniSTS:474482

D9S1983 (e-PCR)
- UniSTS:48599

RH80223 (e-PCR)
- UniSTS:85737

D9S1827 (e-PCR)
- UniSTS:25084

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GDP binding	ISS Inferred from Sequence or Structural Similarity more info
enables GTP binding	IEA Inferred from Electronic Annotation more info
enables GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
enables GTPase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables membrane scission GTPase motor activity	IEA Inferred from Electronic Annotation more info
enables microtubule binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol-3,4,5-trisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-4,5-bisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-4,5-bisphosphate binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein kinase binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in clathrin coat assembly involved in endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endocytosis	TAS Traceable Author Statement more info	PubMed
involved_in endosome organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in modulation of chemical synaptic transmission	IEA Inferred from Electronic Annotation more info
involved_in protein homooligomerization	IDA Inferred from Direct Assay more info	PubMed
involved_in protein homotetramerization	IDA Inferred from Direct Assay more info	PubMed
involved_in receptor internalization	IBA Inferred from Biological aspect of Ancestor more info
involved_in receptor-mediated endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of vesicle size	ISS Inferred from Sequence or Structural Similarity more info
involved_in synaptic vesicle budding from presynaptic endocytic zone membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle scission	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in chromaffin granule	IEA Inferred from Electronic Annotation more info
located_in clathrin-coated pit	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in endocytic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular exosome	HDA more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
part_of membrane coat	IEA Inferred from Electronic Annotation more info
is_active_in microtubule	IBA Inferred from Biological aspect of Ancestor more info
located_in photoreceptor inner segment	IEA Inferred from Electronic Annotation more info
located_in photoreceptor ribbon synapse	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in presynapse	ISS Inferred from Sequence or Structural Similarity more info
located_in presynaptic endocytic zone membrane	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: dynamin-1

Names: dynamin I

NP_001005336.1

EC 3.6.5.5

NP_001275666.1

EC 3.6.5.5

NP_001275667.1

EC 3.6.5.5

NP_001275668.1

EC 3.6.5.5

NP_001361198.1

EC 3.6.5.5

NP_004399.2

EC 3.6.5.5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029726.1 RefSeqGene

Range

4996..56861

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001005336.3 → NP_001005336.1 dynamin-1 isoform 2

See identical proteins and their annotated locations for NP_001005336.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an alternate exon in the 3' coding region that results in a frameshift and an early stop codon, compared to variant 1. The resulting isoform (2), also known as internal form 2 and the short C-terminal form, is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AI660320, BC050279, BC063850, DA221568

Consensus CDS

CCDS43882.1

UniProtKB/TrEMBL

B7ZAC0

Related

ENSP00000345680.7, ENST00000341179.11

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03378
Location:752 → 844

PHA03378; EBNA-3B; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain
NM_001288737.2 → NP_001275666.1 dynamin-1 isoform 3

See identical proteins and their annotated locations for NP_001275666.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an internal alternate in-frame exon, and contains an alternate in-frame exon, and includes an alternate exon in the 3' coding region that results in a frameshift and an early stop codon, compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 3 and 4 encode the same protein.

Source sequence(s)

AI660320, AK296326, BC050279, BC063850, DA510154, L07810

Consensus CDS

CCDS75911.1

UniProtKB/TrEMBL

B7ZAC0

Related

ENSP00000377219.3, ENST00000393594.7

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03378
Location:752 → 844

PHA03378; EBNA-3B; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain
NM_001288738.2 → NP_001275667.1 dynamin-1 isoform 3

See identical proteins and their annotated locations for NP_001275667.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an internal alternate in-frame exon, and contains an alternate in-frame exon, and includes an alternate exon in the 3' coding region that results in a frameshift and an early stop codon, compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 3 and 4 encode the same protein.

Source sequence(s)

AI660320, AK316235, AL590708, BC050279, BG396820

Consensus CDS

CCDS75911.1

UniProtKB/TrEMBL

B7ZAC0

Related

ENSP00000419225.1, ENST00000475805.5

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03378
Location:752 → 844

PHA03378; EBNA-3B; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain
NM_001288739.2 → NP_001275668.1 dynamin-1 isoform 4

See identical proteins and their annotated locations for NP_001275668.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an internal alternate in-frame exon, and contains an alternate in-frame exon, compared to variant 1. The resulting protein (isoform 4) is the same length as isoform 1 but differs in an internal region compared to isoform 1.

Source sequence(s)

AI660320, AK225179, BC050279, BC063850, DA510154

Consensus CDS

CCDS75912.1

UniProtKB/TrEMBL

A0A0D9SFB1

Related

ENSP00000420045.1, ENST00000486160.3

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03247
Location:747 → 844

PHA03247; large tegument protein UL36; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain
NM_001374269.1 → NP_001361198.1 dynamin-1 isoform 5

Status: REVIEWED

Source sequence(s)

AL590708

Consensus CDS

CCDS94491.1

UniProtKB/TrEMBL

A0A0U1RQP1, A0A994J7J4

Related

ENSP00000516205.1, ENST00000706053.1

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03247
Location:747 → 852

PHA03247; large tegument protein UL36; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain
NM_004408.4 → NP_004399.2 dynamin-1 isoform 1

See identical proteins and their annotated locations for NP_004399.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1). Isoform 1 has been referred to as internal form 1 and the long C-terminal form.

Source sequence(s)

AI660320, BC050279, BC063850, DA221568

Consensus CDS

CCDS6895.1

UniProtKB/Swiss-Prot

A6NLM6, Q05193, Q5SYX0, Q5SYX2, Q6P3T6, Q86VD2

UniProtKB/TrEMBL

A0A0D9SFB1

Related

ENSP00000362014.4, ENST00000372923.8

Conserved Domains (5) summary

smart00053
Location:6 → 245

DYNc; Dynamin, GTPase

PHA03247
Location:747 → 844

PHA03247; large tegument protein UL36; Provisional

cd01256
Location:520 → 629

PH_dynamin; Dynamin pleckstrin homology (PH) domain

pfam01031
Location:216 → 502

Dynamin_M; Dynamin central region

pfam02212
Location:657 → 745

GED; Dynamin GTPase effector domain