DYNC1LI2

dynein cytoplasmic 1 light intermediate chain 2, the group of Dynein 1 complex subunits

Basic information

Region (hg38): 16:66720893-66751609

Previous symbols: [ "DNCLI2" ]

Links

ENSG00000135720 ∙ NCBI:1783 ∙ OMIM:611406 ∙ HGNC:2966 ∙ Uniprot:O43237 ∙ 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 DYNC1LI2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNC1LI2 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				1		1
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	18	1	0

Variants in DYNC1LI2

This is a list of pathogenic ClinVar variants found in the DYNC1LI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-66723771-C-T		not specified	Uncertain significance (Jun 10, 2024)
16-66727724-C-T		not specified	Uncertain significance (Jan 12, 2024)
16-66727726-G-A		not specified	Uncertain significance (May 15, 2024)
16-66728211-G-A		not specified	Uncertain significance (Apr 27, 2024)
16-66729090-C-T		not specified	Uncertain significance (Jun 30, 2022)
16-66730132-C-A		not specified	Uncertain significance (Dec 07, 2023)
16-66730174-A-G		not specified	Uncertain significance (Oct 06, 2024)
16-66732391-C-T		not specified	Uncertain significance (Mar 01, 2023)
16-66732430-G-A		not specified	Uncertain significance (Feb 27, 2024)
16-66734219-C-A		not specified	Uncertain significance (Feb 27, 2023)
16-66734219-C-G		not specified	Uncertain significance (Aug 02, 2021)
16-66736088-A-G		not specified	Uncertain significance (Mar 18, 2024)
16-66736215-G-A		not specified	Uncertain significance (Jan 06, 2023)
16-66742498-G-A		not specified	Uncertain significance (Nov 24, 2024)
16-66742561-C-T		not specified	Uncertain significance (Nov 08, 2022)
16-66742603-C-A		not specified	Uncertain significance (Nov 12, 2021)
16-66742653-T-C		not specified	Uncertain significance (Dec 01, 2022)
16-66742660-G-A		not specified	Uncertain significance (Aug 14, 2023)
16-66749220-C-T		not specified	Uncertain significance (Nov 02, 2023)
16-66749221-T-C		not specified	Uncertain significance (Feb 21, 2024)
16-66749230-G-C		not specified	Uncertain significance (Sep 08, 2024)
16-66749273-T-C			Likely benign (Sep 01, 2022)
16-66751311-C-T		not specified	Uncertain significance (Jul 30, 2023)
16-66751352-G-A			Likely benign (Sep 01, 2022)
16-66751515-G-A		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYNC1LI2	protein_coding	protein_coding	ENST00000258198	13	30906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0165	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	186	274	0.678	0.0000142	3199
Missense in Polyphen		55	105.4	0.52182		1292
Synonymous	-0.304	114	110	1.04	0.00000633	974
Loss of Function	4.15	3	25.7	0.117	0.00000124	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000681	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.
• Pathway: Salmonella infection - Homo sapiens (human);Phagosome - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);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;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)

Recessive Scores

• pRec: 0.0932

Intolerance Scores

• loftool: 0.254
• rvis_EVS: -0.69
• rvis_percentile_EVS: 14.97

Haploinsufficiency Scores

• pHI: 0.345
• hipred: Y
• hipred_score: 0.696
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dync1li2

Zebrafish Information Network

• Gene name: dync1li2
• Affected structure: cell
• Phenotype tag: abnormal
• Phenotype quality: structure

Gene ontology

• Biological process: microtubule cytoskeleton organization;endoplasmic reticulum to Golgi vesicle-mediated transport;microtubule-based movement;antigen processing and presentation of exogenous peptide antigen via MHC class II;protein homooligomerization;centrosome localization;cellular response to nerve growth factor stimulus
• Cellular component: kinetochore;lysosome;late endosome;centrosome;cytosol;cytoplasmic dynein complex;microtubule;membrane
• Molecular function: microtubule motor activity;ATP binding;dynein heavy chain binding