DNM3

dynamin 3, the group of Pleckstrin homology domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:171817886-172418466

Links

ENSG00000197959 ∙ NCBI:26052 ∙ OMIM:611445 ∙ HGNC:29125 ∙ Uniprot:Q9UQ16 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNM3 gene.

• Inborn genetic diseases (26 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNM3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				4	1	5
non coding						0
Total	0	0	27	3	1

Variants in DNM3

This is a list of pathogenic ClinVar variants found in the DNM3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-171841679-A-G		not specified	Uncertain significance (Oct 03, 2022)
1-171921755-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-171921803-C-T		not specified	Uncertain significance (Jul 20, 2021)
1-171987686-A-G		not specified	Uncertain significance (Aug 30, 2021)
1-171988980-A-T		not specified	Uncertain significance (Nov 06, 2023)
1-171988993-T-C		not specified	Uncertain significance (Oct 20, 2021)
1-171988998-G-T		not specified	Uncertain significance (Jul 27, 2022)
1-171989029-G-T		not specified	Uncertain significance (Oct 12, 2022)
1-171989042-G-A		not specified	Uncertain significance (Oct 12, 2021)
1-172033135-A-G		not specified	Uncertain significance (Jan 09, 2024)
1-172033176-G-T		not specified	Uncertain significance (Aug 01, 2022)
1-172033204-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-172033205-G-A			Likely benign (Apr 01, 2023)
1-172038338-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-172038406-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-172038413-A-C		not specified	Uncertain significance (Apr 19, 2023)
1-172038425-C-A			Likely benign (Sep 01, 2023)
1-172042025-G-T		not specified	Uncertain significance (Apr 08, 2022)
1-172042109-A-G		not specified	Uncertain significance (Jan 24, 2023)
1-172044448-A-G		not specified	Uncertain significance (Sep 14, 2021)
1-172048676-A-G		not specified	Uncertain significance (Jun 07, 2023)
1-172048682-C-G		not specified	Uncertain significance (Jun 07, 2023)
1-172068837-C-G		not specified	Uncertain significance (Nov 09, 2023)
1-172068877-G-A		not specified	Uncertain significance (Mar 02, 2023)
1-172068913-G-T			Likely benign (May 19, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNM3	protein_coding	protein_coding	ENST00000358155	21	576986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00242	0.998	124647	0	24	124671	0.0000963

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	314	480	0.654	0.0000260	5650
Missense in Polyphen		104	189.14	0.54984		2300
Synonymous	-0.143	179	177	1.01	0.00000971	1670
Loss of Function	4.22	13	42.8	0.304	0.00000231	508

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000170
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000291	0.000278
European (Non-Finnish)	0.000102	0.0000973
Middle Eastern	0.00	0.00
South Asian	0.000142	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-associated force-producing protein involved in producing microtubule bundles and able to bind and hydrolyze GTP. Most probably involved in vesicular trafficking processes, in particular endocytosis (By similarity). {ECO:0000250}.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);Endocytosis - Homo sapiens (human);Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Synaptic Vesicle Pathway;Developmental Biology;Signal Transduction;Recycling pathway of L1;Vesicle-mediated transport;Membrane Trafficking;Toll-Like Receptors Cascades;MHC class II antigen presentation;Innate Immune System;Immune System;Adaptive Immune System;Retrograde neurotrophin signalling;Clathrin-mediated endocytosis;Signaling by NTRK1 (TRKA);Signaling by NTRKs;L1CAM interactions;Axon guidance;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases (Consensus)

Recessive Scores

• pRec: 0.243

Intolerance Scores

• loftool: 0.338
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.72

Haploinsufficiency Scores

• pHI: 0.255
• hipred: Y
• hipred_score: 0.680
• ghis: 0.653

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.770

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dnm3
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: endocytosis;synapse assembly;synaptic vesicle budding from presynaptic endocytic zone membrane;receptor internalization;filopodium assembly;regulation of synapse structure or activity;positive regulation of filopodium assembly;negative regulation of dendritic spine morphogenesis;postsynaptic neurotransmitter receptor internalization;postsynapse organization;positive regulation of synaptic vesicle recycling
• Cellular component: photoreceptor inner segment;cytoplasm;Golgi apparatus;microtubule;plasma membrane;postsynaptic density;membrane;axon;cytoplasmic vesicle;synaptic cleft;dendritic spine;dendritic spine head;synapse;postsynaptic membrane;perinuclear region of cytoplasm;apical tubulobulbar complex;basal tubulobulbar complex;extracellular exosome;presynapse;postsynaptic endocytic zone membrane;glutamatergic synapse
• Molecular function: GTPase activity;protein binding;GTP binding;microtubule binding;type 1 metabotropic glutamate receptor binding;type 5 metabotropic glutamate receptor binding;nitric-oxide synthase binding;structural constituent of postsynapse