DYNLT2B

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

Basic information

Region (hg38): 3:196291219-196318299

Previous symbols: [ "TCTEX1D2" ]

Links

ENSG00000213123 ∙ NCBI:255758 ∙ OMIM:617353 ∙ HGNC:28482 ∙ Uniprot:Q8WW35 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• short-rib thoracic dysplasia 17 with or without polydactyly (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short-rib thoracic dysplasia 17 with or without polydactyly	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	27021811

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DYNLT2B gene.

• not_provided (48 variants)
• not_specified (10 variants)
• Short-rib_thoracic_dysplasia_17_with_or_without_polydactyly (6 variants)
• DYNLT2B-related_disorder (3 variants)
• Asphyxiating_thoracic_dystrophy_3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNLT2B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152773.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	6	1	9
missense	1		23	1	1	26
nonsense	3					3
start loss						0
frameshift	2					2
splice donor/acceptor (+/-2bp)	1		1			2
Total	7	0	26	7	2

Highest pathogenic variant AF is 0.0000184772

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DYNLT2B	protein_coding	protein_coding	ENST00000325318	5	27081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000321	0.603	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	48	72.0	0.667	0.00000333	924
Missense in Polyphen		13	21.466	0.60562		276
Synonymous	0.697	20	24.4	0.820	0.00000115	249
Loss of Function	0.612	6	7.85	0.764	4.17e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for proper retrograde ciliary transport. {ECO:0000269|PubMed:26044572}.
• Disease: DISEASE: Short-rib thoracic dysplasia 17 with or without polydactyly (SRTD17) [MIM:617405]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269|PubMed:26044572}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.08

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.146
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tctex1d2
• Phenotype: skeleton phenotype; immune system phenotype; hematopoietic system phenotype

Zebrafish Information Network

• Gene name: tctex1d2
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: cilium assembly;regulation of cilium assembly;regulation of intraciliary retrograde transport
• Cellular component: spindle pole;centrosome;cytoplasmic dynein complex;axoneme;interphase microtubule organizing center;ciliary base
• Molecular function: protein binding;dynein intermediate chain binding