DYNLT5

dynein light chain Tctex-type family member 5

Basic information

Region (hg38): 1:66752459-66779047

Previous symbols: [ "TCTEX1D1" ]

Links

ENSG00000152760 ∙ NCBI:200132 ∙ OMIM:619994 ∙ HGNC:26882 ∙ Uniprot:Q8N7M0 ∙ 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 DYNLT5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNLT5 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in DYNLT5

This is a list of pathogenic ClinVar variants found in the DYNLT5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-66754676-T-A		not specified	Uncertain significance (Aug 28, 2024)
1-66754683-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-66754731-A-C		not specified	Uncertain significance (Nov 15, 2024)
1-66754734-A-C		not specified	Uncertain significance (May 11, 2022)
1-66754740-G-A		not specified	Uncertain significance (Jan 30, 2024)
1-66754750-G-A		not specified	Likely benign (Jan 17, 2024)
1-66754768-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-66770428-G-A		not specified	Uncertain significance (Mar 31, 2024)
1-66776279-G-T		not specified	Uncertain significance (Aug 04, 2021)
1-66776282-C-T		not specified	Uncertain significance (Sep 05, 2024)
1-66776285-C-T		not specified	Uncertain significance (Aug 30, 2022)
1-66776305-A-C		not specified	Uncertain significance (May 31, 2023)
1-66776308-G-A		not specified	Uncertain significance (Nov 13, 2024)
1-66776327-A-G		not specified	Uncertain significance (Dec 03, 2024)
1-66776344-C-G		not specified	Uncertain significance (Oct 05, 2023)
1-66777288-G-A		not specified	Uncertain significance (May 31, 2023)
1-66777414-T-C		not specified	Uncertain significance (Feb 28, 2024)
1-66777419-G-T		not specified	Uncertain significance (Oct 20, 2024)
1-66777431-G-C		not specified	Uncertain significance (Aug 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYNLT5	protein_coding	protein_coding	ENST00000282670	4	26329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000547	0.464	94982	2428	28313	125723	0.131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.398	87	98.1	0.887	0.00000499	1182
Missense in Polyphen		25	24.394	1.0248		335
Synonymous	-0.918	38	31.5	1.21	0.00000150	328
Loss of Function	0.398	7	8.23	0.850	4.26e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.168	0.167
Ashkenazi Jewish	0.187	0.182
East Asian	0.143	0.139
Finnish	0.138	0.137
European (Non-Finnish)	0.141	0.138
Middle Eastern	0.143	0.139
South Asian	0.176	0.163
Other	0.137	0.134

dbNSFP

Source: dbNSFP

• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Intolerance Scores

• loftool: 0.632
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.0595
• hipred: N
• hipred_score: 0.209

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00427

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tctex1d1

Zebrafish Information Network

• Gene name: tctex1d1
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Molecular function: protein binding