DCTN2

dynactin subunit 2, the group of Dynactin subunits

Basic information

Region (hg38): 12:57529632-57547224

Links

ENSG00000175203 ∙ NCBI:10540 ∙ OMIM:607376 ∙ HGNC:2712 ∙ Uniprot:Q13561 ∙ 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 DCTN2 gene.

• not provided (4 variants)
• Inborn genetic diseases (3 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCTN2 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			6	1	1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	1

Variants in DCTN2

This is a list of pathogenic ClinVar variants found in the DCTN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57530703-T-G			Benign (Feb 01, 2024)
12-57530751-G-C			Uncertain significance (Dec 01, 2017)
12-57530760-G-A		not specified	Conflicting classifications of pathogenicity (Jan 01, 2024)
12-57532008-C-T			Uncertain significance (Feb 01, 2024)
12-57532803-A-G			Benign (Aug 01, 2022)
12-57533300-C-T			Likely benign (Jul 01, 2022)
12-57533976-C-T		not specified	Uncertain significance (Apr 04, 2023)
12-57534050-G-A		not specified	Uncertain significance (Sep 23, 2023)
12-57534059-T-G		not specified	Uncertain significance (Jul 14, 2021)
12-57534313-T-A		See cases	Uncertain significance (-)
12-57535097-G-A		Charcot-Marie-Tooth disease	Uncertain significance (Dec 14, 2015)
12-57535502-T-A		not specified	Uncertain significance (Sep 29, 2022)
12-57547045-C-A			Uncertain significance (Jul 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCTN2	protein_coding	protein_coding	ENST00000434715	16	17230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00347	124635	0	3	124638	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	139	218	0.637	0.0000116	2607
Missense in Polyphen		29	67.894	0.42714		796
Synonymous	0.570	76	82.6	0.920	0.00000425	798
Loss of Function	4.31	2	25.5	0.0784	0.00000108	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000928	0.0000464
European (Non-Finnish)	0.00000887	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organization during mitosis. Involved in anchoring microtubules to centrosomes. May play a role in synapse formation during brain development.
• Pathway: Vasopressin-regulated water reabsorption - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);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: 0.347

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.709
• hipred: Y
• hipred_score: 0.662
• ghis: 0.520

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.710

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dctn2
• 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)

Zebrafish Information Network

• Gene name: dctn2
• Affected structure: neuromast hair cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;mitotic cell cycle;endoplasmic reticulum to Golgi vesicle-mediated transport;mitotic spindle organization;cell population proliferation;regulation of G2/M transition of mitotic cell cycle;antigen processing and presentation of exogenous peptide antigen via MHC class II;melanosome transport;protein localization to centrosome;ciliary basal body-plasma membrane docking
• Cellular component: kinetochore;cytoplasm;centrosome;cytosol;dynactin complex;microtubule;membrane;dynein complex;growth cone;vesicle;extracellular exosome
• Molecular function: motor activity;protein binding;protein kinase binding;spectrin binding;identical protein binding