DYNC2I1

dynein 2 intermediate chain 1, the group of Cilia and flagella associated|Dynein 2 complex subunits|WD repeat domain containing

Basic information

Region (hg38): 7:158856558-158956747

Previous symbols: [ "WDR60" ]

Links

ENSG00000126870NCBI:55112OMIM:615462HGNC:21862Uniprot:Q8WVS4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • short-rib thoracic dysplasia 8 with or without polydactyly (Strong), mode of inheritance: AR
  • Jeune syndrome (Supportive), mode of inheritance: AR
  • short rib-polydactyly syndrome, Verma-Naumoff type (Supportive), mode of inheritance: AR
  • short-rib thoracic dysplasia 8 with or without polydactyly (Strong), mode of inheritance: AR
  • short-rib thoracic dysplasia 8 with or without polydactyly (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Short-rib thoracic dysplasia 8 with or without polydactylyARGeneralGenetic knowledge may potentially be beneficial related to manifestations such as renal issues; 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 testingCardiovascular; Gastrointestinal; Genitourinary; Musculoskeletal; Pulmonary; Renal23910462
The condition may involve multiple malformations

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DYNC2I1 gene.

  • Short-rib_thoracic_dysplasia_8_with_or_without_polydactyly (410 variants)
  • Inborn_genetic_diseases (168 variants)
  • not_provided (50 variants)
  • DYNC2I1-related_disorder (27 variants)
  • Asphyxiating_thoracic_dystrophy_3 (4 variants)
  • not_specified (3 variants)
  • See_cases (3 variants)
  • Jeune_thoracic_dystrophy (2 variants)
  • Cystic_renal_disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNC2I1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018051.5. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
119
clinvar
11
clinvar
132
missense
1
clinvar
3
clinvar
230
clinvar
31
clinvar
9
clinvar
274
nonsense
6
clinvar
3
clinvar
1
clinvar
10
start loss
0
frameshift
6
clinvar
4
clinvar
1
clinvar
11
splice donor/acceptor (+/-2bp)
3
clinvar
2
clinvar
1
clinvar
6
Total 13 13 236 150 21

Highest pathogenic variant AF is 0.000172956

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DYNC2I1protein_codingprotein_codingENST00000407559 25100170
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.32e-121.0012447601691246450.000678
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4225485770.9510.00003287008
Missense in Polyphen3761.2890.6037708
Synonymous0.8632092250.9270.00001451949
Loss of Function3.662959.50.4880.00000336707

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001400.00126
Ashkenazi Jewish0.007560.00758
East Asian0.0005640.000556
Finnish0.000.00
European (Non-Finnish)0.0003650.000327
Middle Eastern0.0005640.000556
South Asian0.0003050.000294
Other0.0009970.000992

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play a role in ciliogenesis. {ECO:0000269|PubMed:23910462}.;
Pathway
Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

pRec
0.0922

Intolerance Scores

loftool
0.751
rvis_EVS
1.21
rvis_percentile_EVS
93.05

Haploinsufficiency Scores

pHI
0.112
hipred
N
hipred_score
0.270
ghis
0.472

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.713

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Wdr60
Phenotype

Gene ontology

Biological process
microtubule-based movement;intraciliary transport involved in cilium assembly;embryonic skeletal system morphogenesis;cilium assembly
Cellular component
pericentriolar material;spindle pole;extracellular space;centrosome;cytoplasmic dynein complex;cilium;dynein complex;interphase microtubule organizing center;ciliary tip;ciliary base
Molecular function
protein binding;ATP-dependent microtubule motor activity, plus-end-directed;dynein light chain binding;dynein heavy chain binding