DYNC1LI1

dynein cytoplasmic 1 light intermediate chain 1, the group of Dynein 1 complex subunits

Basic information

Region (hg38): 3:32525974-32570858

Previous symbols: [ "DNCLI1" ]

Links

ENSG00000144635 ∙ NCBI:51143 ∙ OMIM:615890 ∙ HGNC:18745 ∙ Uniprot:Q9Y6G9 ∙ 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 DYNC1LI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNC1LI1 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in DYNC1LI1

This is a list of pathogenic ClinVar variants found in the DYNC1LI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-32526818-G-A		not specified	Uncertain significance (Jan 04, 2025)
3-32526824-G-C		not specified	Uncertain significance (Aug 15, 2023)
3-32526884-T-C		not specified	Uncertain significance (Dec 22, 2023)
3-32526899-G-A		not specified	Uncertain significance (Nov 11, 2024)
3-32526900-G-A		not specified	Uncertain significance (Apr 23, 2024)
3-32528467-G-C			not provided (-)
3-32529611-G-C		not specified	Uncertain significance (May 25, 2022)
3-32529611-G-T		not specified	Uncertain significance (Apr 06, 2023)
3-32530472-T-A		not specified	Uncertain significance (Jan 08, 2025)
3-32530496-C-T		not specified	Uncertain significance (Apr 18, 2023)
3-32533005-G-A		not specified	Uncertain significance (Jul 14, 2021)
3-32534527-T-C		not specified	Uncertain significance (Jan 29, 2024)
3-32534538-A-G		not specified	Uncertain significance (Jun 28, 2023)
3-32534565-T-G		not specified	Uncertain significance (Nov 14, 2024)
3-32534646-T-A		not specified	Uncertain significance (Feb 17, 2022)
3-32537012-C-G		not specified	Uncertain significance (Mar 06, 2025)
3-32537024-C-G		not specified	Uncertain significance (Sep 23, 2023)
3-32537074-G-A		not specified	Uncertain significance (Dec 11, 2024)
3-32537095-T-C		not specified	Uncertain significance (Oct 20, 2024)
3-32541081-G-A		not specified	Uncertain significance (Feb 26, 2024)
3-32541089-G-A		not specified	Uncertain significance (Feb 06, 2024)
3-32541161-G-A		not specified	Uncertain significance (Oct 12, 2022)
3-32541162-G-A		not specified	Uncertain significance (Dec 23, 2024)
3-32541168-C-G		not specified	Uncertain significance (Mar 29, 2022)
3-32541176-G-A		not specified	Uncertain significance (Feb 03, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYNC1LI1	protein_coding	protein_coding	ENST00000273130	13	44904

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0365	125729	0	17	125746	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	221	269	0.822	0.0000125	3361
Missense in Polyphen		47	72.026	0.65254		950
Synonymous	0.657	94	102	0.917	0.00000521	1039
Loss of Function	4.20	4	27.9	0.143	0.00000142	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000109
Finnish	0.0000499	0.0000462
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000116	0.000109
South Asian	0.0000821	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. Cytoplasmic dynein 1 acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. May play a role in binding dynein to membranous organelles or chromosomes. Probably involved in the microtubule-dependent transport of pericentrin. Is required for progress through the spindle assembly checkpoint. The phosphorylated form appears to be involved in the selective removal of MAD1L1 and MAD1L2 but not BUB1B from kinetochores. {ECO:0000269|PubMed:19229290}.
• Pathway: Salmonella infection - Homo sapiens (human);Phagosome - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Neutrophil degranulation;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Innate Immune System;Immune System;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Mitotic Prometaphase;COPI-mediated anterograde transport;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;ER to Golgi Anterograde Transport;Cell Cycle, Mitotic;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Intolerance Scores

• loftool: 0.319
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.2

Haploinsufficiency Scores

• pHI: 0.810
• hipred: Y
• hipred_score: 0.640
• ghis: 0.489

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dync1li1
• Phenotype: cellular phenotype; digestive/alimentary 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: dync1li1
• Affected structure: cell
• Phenotype tag: abnormal
• Phenotype quality: broken

Gene ontology

• Biological process: microtubule cytoskeleton organization;endoplasmic reticulum to Golgi vesicle-mediated transport;microtubule-based movement;cell cycle;viral process;antigen processing and presentation of exogenous peptide antigen via MHC class II;neutrophil degranulation;cell division;positive regulation of mitotic cell cycle spindle assembly checkpoint
• Cellular component: kinetochore;condensed chromosome kinetochore;spindle pole;centrosome;cytosol;cytoplasmic dynein complex;microtubule;plasma membrane;membrane;secretory granule membrane;ficolin-1-rich granule membrane
• Molecular function: RNA binding;microtubule motor activity;protein binding;ATP binding;GTP binding;GDP binding;dynein heavy chain binding