DCTN3

dynactin subunit 3, the group of Dynactin subunits

Basic information

Region (hg38): 9:34613544-34620523

Links

ENSG00000137100 ∙ NCBI:11258 ∙ OMIM:607387 ∙ HGNC:2713 ∙ Uniprot:O75935 ∙ 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 DCTN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCTN3 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						0
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in DCTN3

This is a list of pathogenic ClinVar variants found in the DCTN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34613846-A-G		not specified	Uncertain significance (Oct 22, 2021)
9-34614070-T-C		not specified	Uncertain significance (Jun 02, 2023)
9-34616089-A-G		not specified	Uncertain significance (Jan 25, 2023)
9-34617929-C-A		not specified	Uncertain significance (Jan 10, 2023)
9-34617933-C-T		not specified	Uncertain significance (Oct 20, 2023)
9-34617955-C-A		not specified	Uncertain significance (Feb 12, 2024)
9-34618735-T-C		not specified	Uncertain significance (Jun 27, 2022)
9-34618752-G-T		not specified	Uncertain significance (Mar 29, 2024)
9-34620398-C-G		not specified	Uncertain significance (Oct 27, 2022)
9-34620425-C-T		not specified	Uncertain significance (Jul 20, 2021)
9-34620427-C-A		not specified	Uncertain significance (Feb 10, 2023)
9-34620442-T-C		not specified	Uncertain significance (May 04, 2023)
9-34620449-C-T		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCTN3	protein_coding	protein_coding	ENST00000259632	7	6968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-7	0.209	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.350	96	106	0.904	0.00000563	1197
Missense in Polyphen		30	35.906	0.83553		445
Synonymous	-0.301	45	42.5	1.06	0.00000226	362
Loss of Function	0.205	11	11.8	0.935	5.04e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.0000969	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Together with dynein may be involved in spindle assembly and cytokinesis. {ECO:0000269|PubMed:9722614}.
• Pathway: Vesicle-mediated transport;lissencephaly gene (lis1) in neuronal migration and development;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Regulation of PLK1 Activity at G2/M Transition;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;COPI-mediated anterograde transport;M Phase;Cell Cycle;ER to Golgi Anterograde Transport;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Intra-Golgi and retrograde Golgi-to-ER traffic;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.264
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.0896
• hipred: N
• hipred_score: 0.332
• ghis: 0.592

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dctn3

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;mitotic cell cycle;endoplasmic reticulum to Golgi vesicle-mediated transport;microtubule-based process;regulation of G2/M transition of mitotic cell cycle;antigen processing and presentation of exogenous peptide antigen via MHC class II;cytoskeleton-dependent cytokinesis;ciliary basal body-plasma membrane docking
• Cellular component: condensed chromosome kinetochore;nucleolus;centrosome;spindle;cytosol;dynactin complex;microtubule;midbody;cleavage furrow;perinuclear region of cytoplasm
• Molecular function: structural molecule activity;protein binding