KIF1B
kinesin family member 1B, the group of Pleckstrin homology domain containing|MicroRNA protein coding host genes|Kinesins
Basic information
Region (hg38): 1:10210570-10381603
Previous symbols: [ "CMT2A", "CMT2" ]
Links
Phenotypes
GenCC
Source:
- neuroblastoma, susceptibility to, 1 (Limited), mode of inheritance: AD
- pheochromocytoma (Moderate), mode of inheritance: AD
- Charcot-Marie-Tooth disease type 2A1 (Limited), mode of inheritance: AD
- hereditary pheochromocytoma-paraganglioma (Supportive), mode of inheritance: AD
- Charcot-Marie-Tooth disease type 2A1 (Supportive), mode of inheritance: AD
- Charcot-Marie-Tooth disease type 2A1 (Limited), mode of inheritance: AD
- pheochromocytoma (Limited), mode of inheritance: AD
- Charcot-Marie-Tooth disease type 2A1 (No Known Disease Relationship), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Neuroblastoma, susceptibility to 1; Pheochromocytoma | AD | Oncologic | Surveillance and/or awareness of cancer risk may allow early diagnosis and treatment of tumors, which may reduce morbidity and mortality | Neurologic; Oncologic | 9409358; 11389829; 18334619; 24102379 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (2900 variants)
- Charcot-Marie-Tooth_disease_type_2 (1299 variants)
- not_provided (187 variants)
- Charcot-Marie-Tooth_disease (107 variants)
- Charcot-Marie-Tooth_disease_type_2A1 (97 variants)
- KIF1B-related_disorder (90 variants)
- Neuroblastoma,_susceptibility_to,_1 (85 variants)
- Neuroblastoma (85 variants)
- Pheochromocytoma (37 variants)
- Meniere_disease (4 variants)
- Hereditary_cancer-predisposing_syndrome (4 variants)
- Intellectual_disability (2 variants)
- Charcot-Marie-Tooth_disease_type_4 (2 variants)
- Hereditary_cancer (2 variants)
- Charcot-Marie-Tooth_disease,_type_I (2 variants)
- Ovarian_cancer (2 variants)
- Malignant_tumor_of_breast (2 variants)
- EMG_abnormality (2 variants)
- Upper_limb_undergrowth (1 variants)
- EMG:_myopathic_abnormalities (1 variants)
- Distal_muscle_weakness (1 variants)
- EEG_abnormality (1 variants)
- Short_lower_limbs (1 variants)
- Vitiligo (1 variants)
- Pain (1 variants)
- Scoliosis (1 variants)
- Adrenal_pheochromocytoma (1 variants)
- NEUROBLASTOMA,_SUSCEPTIBILITY_TO,_1,_INCLUDED (1 variants)
- Exaggerated_startle_response (1 variants)
- EMG:_axonal_abnormality (1 variants)
- Arthrogryposis_multiplex_congenita (1 variants)
- Decreased_muscle_mass (1 variants)
- Adult-onset_proximal_spinal_muscular_atrophy,_autosomal_dominant (1 variants)
- Global_developmental_delay (1 variants)
- Hemihypertrophy (1 variants)
- Recurrent_paroxysmal_headache (1 variants)
- Congenital_contracture (1 variants)
- Multiple_endocrine_neoplasia_type_2A (1 variants)
- Gait_ataxia (1 variants)
- Joint_laxity (1 variants)
- Palpitations (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_001365951.3. 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 | 27 | 989 | 1020 | |||
| missense | 1807 | 108 | 1922 | |||
| nonsense | 26 | 27 | ||||
| start loss | 0 | |||||
| frameshift | 25 | 25 | ||||
| splice donor/acceptor (+/-2bp) | 19 | 21 | ||||
| Total | 1 | 3 | 1904 | 1099 | 8 |
Highest pathogenic variant AF is 0.0000099138115
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KIF1B | protein_coding | protein_coding | ENST00000263934 | 46 | 170799 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 6.88e-10 | 125727 | 0 | 20 | 125747 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.60 | 663 | 980 | 0.676 | 0.0000595 | 11646 |
| Missense in Polyphen | 310 | 550.14 | 0.5635 | 6395 | ||
| Synonymous | 0.169 | 348 | 352 | 0.989 | 0.0000211 | 3361 |
| Loss of Function | 8.57 | 11 | 106 | 0.103 | 0.00000647 | 1209 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000867 | 0.0000867 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000883 | 0.0000879 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Motor for anterograde transport of mitochondria. Has a microtubule plus end-directed motility. Isoform 2 is required for induction of neuronal apoptosis. {ECO:0000269|PubMed:18334619}.;
- Disease
- DISEASE: Neuroblastoma 1 (NBLST1) [MIM:256700]: A common neoplasm of early childhood arising from embryonic cells that form the primitive neural crest and give rise to the adrenal medulla and the sympathetic nervous system. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Pheochromocytoma (PCC) [MIM:171300]: A catecholamine- producing tumor of chromaffin tissue of the adrenal medulla or sympathetic paraganglia. The cardinal symptom, reflecting the increased secretion of epinephrine and norepinephrine, is hypertension, which may be persistent or intermittent. {ECO:0000269|PubMed:18334619}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- 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
- 0.274
Intolerance Scores
- loftool
- 0.206
- rvis_EVS
- -1.45
- rvis_percentile_EVS
- 3.93
Haploinsufficiency Scores
- pHI
- 0.201
- hipred
- Y
- hipred_score
- 0.613
- ghis
- 0.561
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.958
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kif1b
- Phenotype
- homeostasis/metabolism phenotype; craniofacial phenotype; muscle phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; hematopoietic 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); 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- kif1b
- Affected structure
- thrombocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- apoptotic process;microtubule-based movement;neuron-neuron synaptic transmission;neuromuscular synaptic transmission;anterograde axonal transport;positive regulation of gene expression;vesicle-mediated transport;cytoskeleton-dependent intracellular transport;lysosome localization;mitochondrion transport along microtubule;response to rotenone;anterograde neuronal dense core vesicle transport;retrograde neuronal dense core vesicle transport;cellular response to nerve growth factor stimulus;protein localization to cell periphery
- Cellular component
- mitochondrion;kinesin complex;microtubule;microtubule associated complex;axon;dendrite;cytoplasmic vesicle membrane;cytoplasmic vesicle;neuron projection;axon cytoplasm
- Molecular function
- microtubule motor activity;protein binding;ATP binding;microtubule binding;ATP-dependent microtubule motor activity, plus-end-directed;ATPase activity;kinesin binding;kinase binding;scaffold protein binding