IFT74
Basic information
Region (hg38): 9:26947039-27066134
Previous symbols: [ "CCDC2" ]
Links
Phenotypes
GenCC
Source:
- Bardet-Biedl syndrome (Supportive), mode of inheritance: AR
- Bardet-Biedl syndrome 22 (Limited), mode of inheritance: AR
- spermatogenic failure 58 (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Bardet-Biedl syndrome 22 | AR | Endocrine | Medical management of obesity with melanocortin-4 receptor (MC4R) agonist (setmelanotide) may be beneficial | Craniofacial; Endocrine; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic | 27486776; 33531668; 33689014; 34539760; 36356613 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (23 variants)
- IFT74-related disorder (3 variants)
- Joubert syndrome 40 (1 variants)
- Spermatogenic failure 58 (1 variants)
- Multiple Morphological Anomalies of Sperm Flagella (MMAF) (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFT74 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 | 84 | 89 | ||||
| missense | 191 | 205 | ||||
| nonsense | 15 | 18 | ||||
| start loss | 1 | |||||
| frameshift | 9 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 10 | 15 | ||||
| splice region | 14 | 20 | 5 | 39 | ||
| non coding | 24 | 75 | 34 | 133 | ||
| Total | 25 | 14 | 222 | 164 | 46 |
Highest pathogenic variant AF is 0.000105
Variants in IFT74
This is a list of pathogenic ClinVar variants found in the IFT74 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IFT74 | protein_coding | protein_coding | ENST00000443698 | 19 | 115892 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.72e-13 | 0.943 | 124637 | 0 | 157 | 124794 | 0.000629 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.07 | 348 | 296 | 1.17 | 0.0000144 | 3989 |
| Missense in Polyphen | 67 | 59.107 | 1.1335 | 791 | ||
| Synonymous | -0.299 | 97 | 93.3 | 1.04 | 0.00000447 | 990 |
| Loss of Function | 2.17 | 26 | 41.0 | 0.634 | 0.00000212 | 507 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000905 | 0.000886 |
| Ashkenazi Jewish | 0.000304 | 0.000298 |
| East Asian | 0.000229 | 0.000223 |
| Finnish | 0.000140 | 0.000139 |
| European (Non-Finnish) | 0.00107 | 0.00106 |
| Middle Eastern | 0.000229 | 0.000223 |
| South Asian | 0.000101 | 0.0000980 |
| Other | 0.000501 | 0.000495 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the intraflagellar transport (IFT) complex B: together with IFT81, forms a tubulin-binding module that specifically mediates transport of tubulin within the cilium. Binds beta-tubulin via its basic region. Required for ciliogenesis. {ECO:0000269|PubMed:23990561}.;
- Pathway
- Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.0851
Intolerance Scores
- loftool
- 0.962
- rvis_EVS
- 1.2
- rvis_percentile_EVS
- 92.98
Haploinsufficiency Scores
- pHI
- 0.287
- hipred
- N
- hipred_score
- 0.425
- ghis
- 0.459
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.164
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Ift74
- Phenotype
- growth/size/body region phenotype; respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- ift74
- Affected structure
- pronephric proximal convoluted tubule
- Phenotype tag
- abnormal
- Phenotype quality
- increased diameter
Gene ontology
- Biological process
- keratinocyte development;Notch signaling pathway;determination of left/right symmetry;heart development;positive regulation of cell adhesion mediated by integrin;intraciliary transport involved in cilium assembly;positive regulation of transcription by RNA polymerase II;negative regulation of epithelial cell proliferation;cilium assembly;non-motile cilium assembly
- Cellular component
- nucleus;centrosome;cilium;intraciliary transport particle B;cytoplasmic vesicle;motile cilium;ciliary tip
- Molecular function
- chromatin binding;protein binding;beta-tubulin binding