DYNLT1

dynein light chain Tctex-type 1, the group of Dyneins, axonemal outer arm complex subunits|Dynein 1 complex subunits|Dynein 2 complex subunits

Basic information

Region (hg38): 6:158636473-158644743

Previous symbols: [ "TCTEL1" ]

Links

ENSG00000146425

∙ NCBI:6993 ∙ OMIM:601554 ∙ HGNC:11697 ∙ Uniprot:P63172 ∙ 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 DYNLT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNLT1 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			7 clinvar			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in DYNLT1

This is a list of pathogenic ClinVar variants found in the DYNLT1 region.

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

Position	Phenotype	Significance	ClinVar
6-158636832-T-C	not specified	Uncertain significance (Jun 16, 2024)	3274208
6-158636894-C-T	not specified	Uncertain significance (Apr 07, 2022)	2404446
6-158637804-G-A	not specified	Uncertain significance (Apr 25, 2022)	2285940
6-158637851-T-C	not specified	Uncertain significance (Jan 18, 2023)	2476368
6-158637879-T-C	not specified	Uncertain significance (Feb 07, 2023)	2461130
6-158637889-T-C	not specified	Uncertain significance (Feb 17, 2024)	3086557
6-158641327-C-A	not specified	Uncertain significance (Apr 22, 2022)	2360712
6-158641347-A-C	not specified	Uncertain significance (May 15, 2024)	3274209
6-158644696-G-C	not specified	Uncertain significance (Jun 07, 2023)	2558943

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYNLT1	protein_coding	protein_coding	ENST00000367089	5	8266

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000732	0.524	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.266	69	63.1	1.09	0.00000327	746
Missense in Polyphen		7	12.002	0.58323		163
Synonymous	-1.58	29	20.0	1.45	0.00000110	188
Loss of Function	0.530	7	8.68	0.806	4.55e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000301	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000545	0.0000544
South Asian	0.000197	0.000196
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. Binds to transport cargos and is involved in apical cargo transport such as rhodopsin-bearing vesicles in polarized epithelia. May also be a accessory component of axonemal dynein.; FUNCTION: (Microbial infection) Is involved in intracellular targeting of D-type retrovirus gag polyproteins to the cytoplasmic assembly site. {ECO:0000269|PubMed:18647839}.;
Pathway: Neutrophil degranulation;Innate Immune System;Immune System;Neurotrophic factor-mediated Trk receptor signaling;Lissencephaly gene (LIS1) in neuronal migration and development (Consensus)

Recessive Scores

pRec: 0.240

Intolerance Scores

loftool: 0.642
rvis_EVS: -0.12
rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

pHI: 0.371
hipred: Y
hipred_score: 0.611
ghis: 0.596

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.834

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Dynlt1f
Phenotype

Gene ontology

Biological process: establishment of mitotic spindle orientation;regulation of G protein-coupled receptor signaling pathway;positive regulation of neuron projection development;dendrite development;intracellular transport of viral protein in host cell;positive regulation of Rac protein signal transduction;negative regulation of mitochondrial membrane permeability;regulation of GTPase activity;neutrophil degranulation;viral entry into host cell;neuron projection morphogenesis;negative regulation of neurogenesis;cell division;regulation of cytoskeleton organization;negative regulation of cell death;axon development;microtubule-dependent intracellular transport of viral material towards nucleus
Cellular component: extracellular region;mitochondrion;Golgi apparatus;spindle;cytoplasmic dynein complex;cytoplasmic microtubule;lamellipodium;secretory granule lumen;neuronal cell body;host cell;axonal growth cone;secretory vesicle;ficolin-1-rich granule lumen
Molecular function: motor activity;protein binding;protein C-terminus binding;identical protein binding