IFT20
Basic information
Region (hg38): 17:28328325-28335489
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (18 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT20 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001267776.2. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 17 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IFT20 | protein_coding | protein_coding | ENST00000585089 | 5 | 7164 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.103 | 0.868 | 125696 | 0 | 2 | 125698 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.115 | 77 | 79.9 | 0.964 | 0.00000375 | 1041 |
| Missense in Polyphen | 11 | 16.93 | 0.64975 | 256 | ||
| Synonymous | 0.394 | 24 | 26.6 | 0.903 | 0.00000121 | 280 |
| Loss of Function | 1.87 | 3 | 9.08 | 0.330 | 3.82e-7 | 114 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000898 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Part of intraflagellar transport (IFT) particles involved in ciliary process assembly. May play a role in the trafficking of ciliary membrane proteins from the Golgi complex to the cilium. Also involved in autophagy since it is required for trafficking of ATG16L and the expansion of the autophagic compartment. {ECO:0000269|PubMed:16775004}.;
- Pathway
- Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.371
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.192
- hipred
- N
- hipred_score
- 0.443
- ghis
- 0.514
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.936
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ift20
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); renal/urinary system phenotype;
Zebrafish Information Network
- Gene name
- ift20
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- curved ventral
Gene ontology
- Biological process
- establishment of planar polarity;kidney development;smoothened signaling pathway;spermatogenesis;visual learning;protein localization to Golgi apparatus;intraciliary transport involved in cilium assembly;photoreceptor cell outer segment organization;opsin transport;intraciliary transport;centrosome localization;cardiac muscle cell differentiation;inner ear receptor cell stereocilium organization;cilium assembly;regulation of canonical Wnt signaling pathway;neural precursor cell proliferation;protein localization to cilium;protein localization to plasma membrane;cochlea development;regulation of cilium assembly;regulation of platelet-derived growth factor receptor-alpha signaling pathway;regulation of autophagosome assembly
- Cellular component
- Golgi membrane;photoreceptor outer segment;Golgi apparatus;cis-Golgi network;centrosome;centriole;microvillus;cilium;intraciliary transport particle B;motile cilium;photoreceptor connecting cilium;stereocilium;dendrite terminus;ciliary tip;ciliary base;kinociliary basal body
- Molecular function
- opsin binding;protein binding;Rab GTPase binding