DCTN5

dynactin subunit 5, the group of Dynactin subunits

Basic information

Region (hg38): 16:23641466-23677472

Links

ENSG00000166847 ∙ NCBI:84516 ∙ OMIM:612962 ∙ HGNC:24594 ∙ Uniprot:Q9BTE1 ∙ 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 DCTN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCTN5 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	0	1

Variants in DCTN5

This is a list of pathogenic ClinVar variants found in the DCTN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-23641516-C-G		Familial cancer of breast	Benign (May 13, 2019)
16-23641558-C-G		not specified	Uncertain significance (Dec 19, 2023)
16-23641699-A-G			Benign (Jan 10, 2019)
16-23661223-G-T		not specified	Uncertain significance (Nov 28, 2024)
16-23661232-A-G		not specified	Uncertain significance (Feb 12, 2024)
16-23661249-T-C		not specified	Uncertain significance (Jun 13, 2024)
16-23661253-A-G		not specified	Uncertain significance (Sep 06, 2022)
16-23665629-C-T		not specified	Uncertain significance (Aug 22, 2023)
16-23665633-G-A		not specified	Uncertain significance (Jul 02, 2024)
16-23665655-C-G		not specified	Uncertain significance (Feb 16, 2023)
16-23665674-G-T		not specified	Uncertain significance (Dec 27, 2023)
16-23665698-C-G		not specified	Uncertain significance (Dec 14, 2023)
16-23667107-G-A		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCTN5	protein_coding	protein_coding	ENST00000300087	6	28483

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00705	0.927	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	57	106	0.538	0.00000581	1190
Missense in Polyphen		15	31.772	0.47212		302
Synonymous	1.18	29	38.3	0.757	0.00000209	339
Loss of Function	1.58	5	10.6	0.474	6.15e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Vasopressin-regulated water reabsorption - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.583
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.327
• hipred: Y
• hipred_score: 0.509
• ghis: 0.699

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.975

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dctn5
• Phenotype: skeleton phenotype; renal/urinary system phenotype; vision/eye phenotype; 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: ventricular septum development;endoplasmic reticulum to Golgi vesicle-mediated transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;aorta development;coronary vasculature development
• Cellular component: condensed chromosome kinetochore;nucleoplasm;centrosome;cytosol;nuclear membrane
• Molecular function: protein binding