DYNLT2

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

Basic information

Region (hg38): 6:169740109-169751587

Previous symbols: [ "TCTE3" ]

Links

ENSG00000184786 ∙ NCBI:6991 ∙ OMIM:186977 ∙ HGNC:11695 ∙ Uniprot:Q8IZS6 ∙ 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 DYNLT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNLT2 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			15	3		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	15	4	0

Variants in DYNLT2

This is a list of pathogenic ClinVar variants found in the DYNLT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-169740193-A-G		not specified	Uncertain significance (Jan 09, 2024)
6-169740223-C-T		not specified	Likely benign (Apr 12, 2022)
6-169740225-T-C		not specified	Uncertain significance (Dec 05, 2024)
6-169740291-G-A		not specified	Uncertain significance (Dec 02, 2022)
6-169743135-C-T		not specified	Uncertain significance (May 13, 2024)
6-169743172-G-A		not specified	Uncertain significance (Dec 30, 2024)
6-169743219-T-C		not specified	Uncertain significance (Sep 19, 2023)
6-169743225-T-C		not specified	Uncertain significance (Mar 24, 2023)
6-169744085-C-T		not specified	Likely benign (Jan 26, 2022)
6-169744145-C-A		not specified	Uncertain significance (Jan 02, 2024)
6-169744181-T-C		not specified	Uncertain significance (Nov 21, 2024)
6-169744189-T-C		not specified	Uncertain significance (Apr 22, 2024)
6-169744193-C-T		not specified	Uncertain significance (Apr 13, 2023)
6-169744231-T-C		not specified	Uncertain significance (May 08, 2023)
6-169744247-T-C		not specified	Uncertain significance (Mar 22, 2023)
6-169744258-C-G		not specified	Uncertain significance (Jun 10, 2022)
6-169751344-C-T		not specified	Uncertain significance (May 13, 2024)
6-169751392-C-G		not specified	Likely benign (Apr 20, 2023)
6-169751446-C-T		not specified	Uncertain significance (May 16, 2024)
6-169751469-T-C			Likely benign (Jul 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYNLT2	protein_coding	protein_coding	ENST00000366774	4	11446

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.28e-9	0.0409	125695	1	52	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0444	106	105	1.01	0.00000508	1286
Missense in Polyphen		33	32.929	1.0022		421
Synonymous	0.890	33	40.2	0.821	0.00000201	358
Loss of Function	-0.651	12	9.80	1.22	4.15e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000327	0.000327
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000194	0.000185
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.000110	0.000109
South Asian	0.000398	0.000359
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be an accessory component of axonemal dynein and cytoplasmic dynein 1. Candidate for involvement in male sterility (By similarity). {ECO:0000250}.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.0683

Intolerance Scores

• loftool: 0.857
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0390
• hipred: N
• hipred_score: 0.123
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.335

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcte3
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Cellular component: cytoplasm;microtubule;membrane;dynein complex
• Molecular function: motor activity