DCTN4

dynactin subunit 4, the group of Dynactin subunits

Basic information

Region (hg38): 5:150708439-150759095

Links

ENSG00000132912 ∙ NCBI:51164 ∙ OMIM:614758 ∙ HGNC:15518 ∙ Uniprot:Q9UJW0 ∙ 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 DCTN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCTN4 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					3	3
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	3

Variants in DCTN4

This is a list of pathogenic ClinVar variants found in the DCTN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-150711228-A-G		not specified	Uncertain significance (Nov 09, 2022)
5-150711239-G-T			Benign (Aug 14, 2017)
5-150711240-G-A		not specified	Uncertain significance (Aug 21, 2023)
5-150711262-C-G		not specified	Uncertain significance (Sep 16, 2021)
5-150711289-C-T		not specified	Uncertain significance (Feb 23, 2023)
5-150711294-C-T		not specified	Uncertain significance (Jun 06, 2023)
5-150711319-T-C		not specified	Uncertain significance (Apr 22, 2022)
5-150715572-C-T		not specified	Uncertain significance (Dec 07, 2021)
5-150715603-A-G			Benign (Aug 08, 2017)
5-150715638-C-T		not specified	Likely benign (Dec 08, 2023)
5-150718286-C-T		not specified	Uncertain significance (May 24, 2023)
5-150719764-A-G			Benign (Sep 15, 2017)
5-150730633-G-A		not specified	Uncertain significance (Oct 04, 2022)
5-150730647-C-T		not specified	Uncertain significance (Jun 05, 2024)
5-150730648-G-A		not specified	Uncertain significance (Feb 14, 2023)
5-150731061-G-A		not specified	Uncertain significance (Feb 28, 2024)
5-150731062-G-A		not specified	Uncertain significance (Feb 13, 2024)
5-150731423-C-T		not specified	Uncertain significance (May 23, 2024)
5-150733420-C-T		not specified	Uncertain significance (Sep 13, 2023)
5-150742116-G-A		not specified	Uncertain significance (Oct 20, 2021)
5-150742149-C-T		not specified	Uncertain significance (Aug 11, 2021)
5-150758899-T-C		not specified	Uncertain significance (Aug 02, 2022)
5-150758929-G-A		not specified	Uncertain significance (Dec 27, 2023)
5-150758933-G-C		not specified	Uncertain significance (Oct 26, 2022)
5-150758968-C-A		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCTN4	protein_coding	protein_coding	ENST00000446090	14	50670

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.732	0.268	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	207	274	0.755	0.0000153	3052
Missense in Polyphen		37	64.419	0.57437		686
Synonymous	-0.417	101	95.8	1.05	0.00000513	880
Loss of Function	4.13	6	30.7	0.195	0.00000177	342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could have a dual role in dynein targeting and in ACTR1A/Arp1 subunit of dynactin pointed-end capping. Could be involved in ACTR1A pointed-end binding and in additional roles in linking dynein and dynactin to the cortical cytoskeleton.
• Pathway: Vasopressin-regulated water reabsorption - Homo sapiens (human);Huntington,s disease - 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: 0.120

Intolerance Scores

• loftool: 0.524
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

• pHI: 0.380
• hipred: Y
• hipred_score: 0.696
• ghis: 0.635

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.861

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dctn4

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;nuclear migration;antigen processing and presentation of exogenous peptide antigen via MHC class II
• Cellular component: kinetochore;spindle pole;stress fiber;nucleus;cytoplasm;centrosome;cytosol;dynactin complex;focal adhesion;cell cortex;sarcomere
• Molecular function: protein binding;protein N-terminus binding