DYNC1I1

dynein cytoplasmic 1 intermediate chain 1, the group of Dynein 1 complex subunits|WD repeat domain containing

Basic information

Region (hg38): 7:95772506-96110322

Previous symbols: [ "DNCI1" ]

Links

ENSG00000158560 ∙ NCBI:1780 ∙ OMIM:603772 ∙ HGNC:2963 ∙ Uniprot:O14576 ∙ 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 DYNC1I1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNC1I1 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				15	6	21
missense			31		3	34
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding				3	25	28
Total	0	0	32	18	34

Variants in DYNC1I1

This is a list of pathogenic ClinVar variants found in the DYNC1I1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-95804758-A-G		not specified	Uncertain significance (Jun 07, 2023)
7-95804762-A-G		DYNC1I1-related disorder	Likely benign (Nov 19, 2023)
7-95804765-G-A			Likely benign (Mar 20, 2023)
7-95804808-C-T			Uncertain significance (Feb 09, 2023)
7-95804844-C-G		not specified • DYNC1I1-related disorder	Benign (Jan 29, 2024)
7-95810385-C-T		not specified	Likely benign (Mar 29, 2016)
7-95810423-A-C		DYNC1I1-related disorder	Benign (Nov 25, 2023)
7-95810428-G-A		not specified	Uncertain significance (Apr 08, 2024)
7-95810470-C-T			Benign (Jul 28, 2023)
7-95810499-G-A		DYNC1I1-related disorder	Benign (Jan 15, 2024)
7-95810516-A-T			Likely benign (Jan 26, 2023)
7-95810675-TG-T			Benign (Jun 03, 2021)
7-95810694-A-AG			Benign (May 11, 2021)
7-95813093-C-CT			Benign (May 20, 2021)
7-95813198-C-G		DYNC1I1-related disorder	Benign (Oct 17, 2023)
7-95813202-C-T		not specified	Uncertain significance (Jan 22, 2024)
7-95813225-A-G		not specified	Uncertain significance (Apr 09, 2024)
7-95813317-C-A		DYNC1I1-related disorder	Likely benign (Jul 19, 2019)
7-95813325-G-C		not specified	Uncertain significance (Nov 23, 2022)
7-95813328-C-T			Uncertain significance (Jun 27, 2022)
7-95813378-T-TA			Benign (May 20, 2021)
7-95813378-T-TAA			Benign (May 20, 2021)
7-95827848-C-T			Benign (May 11, 2021)
7-95827886-C-T			Benign (May 11, 2021)
7-95827912-G-C			Benign (May 25, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYNC1I1	protein_coding	protein_coding	ENST00000324972	16	337769

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.76e-7	1.00	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	251	371	0.677	0.0000206	4217
Missense in Polyphen		103	178.85	0.5759		2048
Synonymous	1.60	116	140	0.828	0.00000824	1218
Loss of Function	3.15	18	39.3	0.458	0.00000210	437

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000209	0.000209
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000972	0.0000967
Middle Eastern	0.000218	0.000217
South Asian	0.000131	0.000131
Other	0.000326	0.000326

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. The intermediate chains mediate the binding of dynein to dynactin via its 150 kDa component (p150- glued) DCNT1. May play a role in mediating the interaction of cytoplasmic dynein with membranous organelles and kinetochores.
• 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: 0.198

Intolerance Scores

• loftool: 0.815
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.72

Haploinsufficiency Scores

• pHI: 0.279
• hipred: Y
• hipred_score: 0.747
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dync1i1

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;microtubule-based movement;antigen processing and presentation of exogenous peptide antigen via MHC class II;vesicle transport along microtubule
• Cellular component: kinetochore;condensed chromosome kinetochore;spindle pole;nucleus;cytoplasm;cytosol;cytoplasmic dynein complex;microtubule;dynein complex;vesicle;cytoplasmic ribonucleoprotein granule;perinuclear region of cytoplasm;recycling endosome
• Molecular function: motor activity;microtubule motor activity;protein binding;microtubule binding;ATP-dependent microtubule motor activity, plus-end-directed;spectrin binding;dynein light chain binding;dynein heavy chain binding