IFT20
intraflagellar transport 20, the group of IFT-B2 complex
Basic information
Region (hg38): 17:28328325-28335489
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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.
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 | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 0 |
Variants in IFT20
This is a list of pathogenic ClinVar variants found in the IFT20 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-28329213-G-T | not specified | Uncertain significance (Apr 11, 2023) | ||
| 17-28329230-T-G | not specified | Uncertain significance (Jan 23, 2023) | ||
| 17-28329246-T-C | not specified | Uncertain significance (May 06, 2022) | ||
| 17-28329264-G-A | not specified | Uncertain significance (Oct 05, 2022) | ||
| 17-28330460-C-G | not specified | Uncertain significance (Jan 19, 2024) | ||
| 17-28330475-G-A | not specified | Uncertain significance (Sep 22, 2022) | ||
| 17-28330504-A-G | not specified | Uncertain significance (Feb 03, 2025) | ||
| 17-28330508-T-C | not specified | Uncertain significance (Dec 27, 2023) | ||
| 17-28331870-T-C | not specified | Uncertain significance (Dec 14, 2023) | ||
| 17-28331871-C-A | not specified | Uncertain significance (Apr 22, 2024) | ||
| 17-28331874-T-C | not specified | Uncertain significance (Feb 09, 2022) | ||
| 17-28331877-A-G | not specified | Uncertain significance (Aug 14, 2024) | ||
| 17-28331952-G-A | not specified | Uncertain significance (Oct 20, 2024) | ||
| 17-28331961-C-T | not specified | Uncertain significance (Oct 14, 2021) | ||
| 17-28331964-C-T | not specified | Uncertain significance (Dec 17, 2024) |
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