DYNLT3

dynein light chain Tctex-type 3, the group of Dyneins, axonemal inner arm I1/f complex subunits|Dynein 1 complex subunits|Dynein 2 complex subunits

Basic information

Region (hg38): X:37836757-37847571

Previous symbols: [ "TCTE1L" ]

Links

ENSG00000165169 ∙ NCBI:6990 ∙ OMIM:300302 ∙ HGNC:11694 ∙ Uniprot:P51808 ∙ 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 DYNLT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNLT3 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			7			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	1

Variants in DYNLT3

This is a list of pathogenic ClinVar variants found in the DYNLT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-37840625-G-A		not specified	Uncertain significance (May 28, 2024)
X-37840649-T-A		not specified	Uncertain significance (Jul 05, 2023)
X-37841079-C-T		not specified	Uncertain significance (Jul 15, 2021)
X-37841795-G-A		not specified	Benign (Mar 29, 2016)
X-37841844-G-A		not specified	Uncertain significance (Feb 05, 2024)
X-37841854-G-C		not specified	Uncertain significance (Dec 13, 2023)
X-37846358-C-G		not specified	Uncertain significance (Aug 28, 2024)
X-37847495-G-C		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYNLT3	protein_coding	protein_coding	ENST00000378578	5	10881

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.719	0.269	122758	1	2	122761	0.0000122

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.117	36	38.0	0.946	0.00000276	771
Missense in Polyphen		11	11.397	0.96513		226
Synonymous	-0.725	17	13.6	1.25	0.00000108	196
Loss of Function	1.90	0	4.18	0.00	2.65e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000799	0.0000627
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000249	0.0000179
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. Probably binds BUB3 as part of transport cargo. Required for the efficient progression through mitosis (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.446
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.0799
• hipred: Y
• hipred_score: 0.592
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.724

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dynlt3

Gene ontology

• Biological process: cell cycle;regulation of mitotic cell cycle;positive regulation of mitotic cell cycle;cell division
• Cellular component: kinetochore;condensed chromosome kinetochore;nucleus;cytoplasmic dynein complex;mitotic spindle astral microtubule
• Molecular function: motor activity;protein binding;identical protein binding