DYNLT4

dynein light chain Tctex-type 4

Basic information

Region (hg38): 1:44805893-44807351

Previous symbols: [ "TCTEX1D4" ]

Links

ENSG00000188396 ∙ NCBI:343521 ∙ OMIM:611713 ∙ HGNC:32315 ∙ Uniprot:Q5JR98 ∙ 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 DYNLT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNLT4 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in DYNLT4

This is a list of pathogenic ClinVar variants found in the DYNLT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-44806020-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-44806028-G-A		not specified	Uncertain significance (Mar 19, 2024)
1-44806038-C-G		Neurodevelopmental disorder	Uncertain significance (-)
1-44806068-A-G		not specified	Uncertain significance (Jun 27, 2022)
1-44806082-C-T		not specified	Uncertain significance (Aug 11, 2022)
1-44806085-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-44806105-G-T		not specified	Uncertain significance (Sep 10, 2024)
1-44806112-A-G		not specified	Uncertain significance (Jul 25, 2024)
1-44806113-C-T		not specified	Uncertain significance (Oct 02, 2023)
1-44806128-C-G		not specified	Uncertain significance (Jun 11, 2024)
1-44806150-A-T		not specified	Uncertain significance (Oct 05, 2021)
1-44806163-T-C		not specified	Uncertain significance (Dec 06, 2024)
1-44806166-T-C		not specified	Uncertain significance (Mar 27, 2023)
1-44806188-G-A		not specified	Uncertain significance (Aug 04, 2024)
1-44806232-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-44806281-C-A		not specified	Uncertain significance (Sep 08, 2023)
1-44806290-G-T		not specified	Uncertain significance (Jan 30, 2024)
1-44806321-C-G		not specified	Uncertain significance (Jan 03, 2024)
1-44806343-C-T		not specified	Uncertain significance (Dec 04, 2024)
1-44806379-G-A		not specified	Uncertain significance (Jul 17, 2023)
1-44806412-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-44806416-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-44806423-G-A			Likely benign (Sep 01, 2022)
1-44806436-C-T		not specified	Uncertain significance (Feb 22, 2024)
1-44806457-C-T		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYNLT4	protein_coding	protein_coding	ENST00000372200	1	1373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0118	0.656	118750	0	1	118751	0.00000421

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.788	95	119	0.797	0.00000953	1283
Missense in Polyphen		31	34.957	0.8868		392
Synonymous	1.86	42	60.4	0.696	0.00000527	520
Loss of Function	0.477	3	4.03	0.744	2.95e-7	47

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000692	0.0000692
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0998

Haploinsufficiency Scores

• pHI: 0.270
• hipred: N
• hipred_score: 0.258
• ghis: 0.391

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tctex1d4

Gene ontology

• Cellular component: acrosomal vesicle;nucleus;microtubule organizing center;axoneme;sperm flagellum
• Molecular function: protein binding;protein phosphatase 1 binding