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 (2 variants)
• Short-rib thoracic dysplasia 17 with or without polydactyly (2 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.

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			2	5		7
missense			19	1	1	21
nonsense	1					1
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region	1		4	2		7
non coding				11	8	19
Total	2	0	22	17	9

Highest pathogenic variant AF is 0.0000329

Variants in DYNLT2B

This is a list of pathogenic ClinVar variants found in the DYNLT2B region.

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

Position	Type	Phenotype	Significance	ClinVar
3-196291331-T-C			Uncertain significance (Jan 22, 2024)
3-196291359-C-T			Uncertain significance (Dec 12, 2021)
3-196291379-A-G			Uncertain significance (May 28, 2022)
3-196291390-AAC-A			Likely benign (Aug 01, 2023)
3-196295879-T-C			Benign (May 15, 2021)
3-196295997-T-C			Likely benign (Oct 29, 2022)
3-196296015-A-G			Likely benign (Apr 23, 2023)
3-196296026-T-C		not specified	Uncertain significance (Jun 28, 2023)
3-196296031-T-C			Uncertain significance (Oct 24, 2022)
3-196296055-C-T		not specified	Uncertain significance (Nov 12, 2021)
3-196296058-C-T		not specified	Uncertain significance (Oct 14, 2023)
3-196296059-G-A		DYNLT2B-related disorder	Likely benign (Jan 29, 2024)
3-196296081-A-G			Likely benign (Jan 18, 2023)
3-196296089-A-G			Likely benign (Apr 04, 2022)
3-196296090-G-T			Benign (May 19, 2021)
3-196296136-C-T			Benign (May 19, 2021)
3-196306926-A-C			Likely benign (Apr 29, 2021)
3-196306938-C-T		DYNLT2B-related disorder	Uncertain significance (Oct 12, 2022)
3-196306939-T-A		Asphyxiating thoracic dystrophy 3 • Short-rib thoracic dysplasia 17 with or without polydactyly	Pathogenic (Mar 14, 2024)
3-196306945-T-C			Likely benign (Dec 05, 2023)
3-196306971-T-A			Uncertain significance (Oct 18, 2022)
3-196306975-T-C			Likely benign (Sep 20, 2021)
3-196306977-C-G			Uncertain significance (Aug 04, 2023)
3-196306985-A-G			Uncertain significance (Jul 19, 2022)
3-196306988-A-G		not specified	Uncertain significance (Dec 27, 2023)

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