KIF16B
Basic information
Region (hg38): 20:16272104-16573448
Previous symbols: [ "C20orf23" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (200 variants)
- not_provided (16 variants)
- Prostate_cancer (2 variants)
- Autism (1 variants)
- Muscular_atrophy (1 variants)
- KIF16B-related_Intellectual_Disability (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF16B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024704.5. 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 4 | |||||
missense | 169 | 178 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 0 | 171 | 9 | 4 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KIF16B | protein_coding | protein_coding | ENST00000408042 | 23 | 301330 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.10e-19 | 0.979 | 125428 | 0 | 320 | 125748 | 0.00127 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.10 | 668 | 753 | 0.887 | 0.0000426 | 9147 |
Missense in Polyphen | 289 | 360.27 | 0.80217 | 4343 | ||
Synonymous | 1.36 | 257 | 286 | 0.898 | 0.0000161 | 2592 |
Loss of Function | 2.68 | 40 | 63.0 | 0.635 | 0.00000301 | 811 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00439 | 0.00430 |
Ashkenazi Jewish | 0.00159 | 0.00159 |
East Asian | 0.00432 | 0.00425 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.00102 | 0.00101 |
Middle Eastern | 0.00432 | 0.00425 |
South Asian | 0.000847 | 0.000817 |
Other | 0.000818 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Plus end-directed microtubule-dependent motor protein involved in endosome transport and receptor recycling and degradation. Regulates the plus end motility of early endosomes and the balance between recycling and degradation of receptors such as EGF receptor (EGFR) and FGF receptor (FGFR). Regulates the Golgi to endosome transport of FGFR-containing vesicles during early development, a key process for developing basement membrane and epiblast and primitive endoderm lineages during early postimplantation development. {ECO:0000269|PubMed:15882625}.;
- 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
(Consensus)
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- 0.928
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.7
Haploinsufficiency Scores
- pHI
- 0.444
- hipred
- N
- hipred_score
- 0.327
- ghis
- 0.487
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0554
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kif16b
- Phenotype
- embryo 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);
Gene ontology
- Biological process
- formation of primary germ layer;regulation of receptor recycling;Golgi to endosome transport;microtubule-based movement;epidermal growth factor receptor signaling pathway;endoderm development;fibroblast growth factor receptor signaling pathway;receptor catabolic process;early endosome to late endosome transport;cellular response to interferon-gamma
- Cellular component
- endosome;early endosome;cytosol;kinesin complex;microtubule;early endosome membrane;phagocytic vesicle
- Molecular function
- microtubule motor activity;ATP binding;phosphatidylinositol-3,4,5-trisphosphate binding;microtubule binding;ATP-dependent microtubule motor activity, plus-end-directed;ATPase activity;Rab GTPase binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-3,4-bisphosphate binding;phosphatidylinositol-3,5-bisphosphate binding