KIF3C
Basic information
Region (hg38): 2:25926598-25982749
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (90 variants)
- KIF3C-related_neurodevelopmental_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF3C gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002254.8. 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 87 | 89 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 88 | 3 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KIF3C | protein_coding | protein_coding | ENST00000264712 | 8 | 56148 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.992 | 0.00847 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.36 | 358 | 508 | 0.705 | 0.0000326 | 5213 |
| Missense in Polyphen | 97 | 184.93 | 0.52451 | 1956 | ||
| Synonymous | 1.31 | 186 | 210 | 0.885 | 0.0000135 | 1598 |
| Loss of Function | 4.58 | 4 | 31.9 | 0.125 | 0.00000178 | 348 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000995 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Microtubule-based anterograde translocator for membranous organelles. {ECO:0000250}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Kinesins;Factors involved in megakaryocyte development and platelet production;Hemostasis;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi and retrograde Golgi-to-ER traffic;Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.254
- rvis_EVS
- -0.75
- rvis_percentile_EVS
- 13.67
Haploinsufficiency Scores
- pHI
- 0.274
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.605
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.674
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kif3c
- 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- kif3cb
- Affected structure
- photoreceptor outer segment layer
- Phenotype tag
- abnormal
- Phenotype quality
- decreased variability of size
Gene ontology
- Biological process
- retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based movement;antigen processing and presentation of exogenous peptide antigen via MHC class II;intraciliary transport involved in cilium assembly;organelle transport along microtubule
- Cellular component
- cytosol;kinesin complex;microtubule;cilium;ciliary tip
- Molecular function
- motor activity;microtubule motor activity;ATP binding;microtubule binding;ATPase activity