KIF2A
protein-codingkinesin family member 2A, the group of Kinesins
Gene summary
The protein encoded by this gene is a plus end-directed motor required for normal mitotic progression. The encoded protein is required for normal spindle activity during mitosis and is necessary for normal brain development. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
- KIF2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~84.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0014170
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0014170
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0014170
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014170
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KIF2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001098511.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | 100 | 5 | 113 | ||
| missense | 2 | 4 | 196 | 40 | 11 | 253 |
| nonsense | 1 | 3 | 1 | 5 | ||
| start loss | 1 | 1 | ||||
| frameshift | 5 | 3 | 8 | |||
| splice donor/acceptor (+/-2bp) | 6 | 1 | 7 | |||
| Total | 3 | 4 | 219 | 145 | 16 | 387 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001091981.1 | 21 | MANE Select | |
| Ensembl | ENSP00000385000.3 | 21 | MANE Select | |
| RefSeq | NP_001230881.2 | 19 | Standard | |
| RefSeq | NP_001230882.1 | 20 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Signal Transduction
- Vesicle-mediated transport
- Membrane Trafficking
- Kinesins
- Factors involved in megakaryocyte development and platelet production
Biological Process
- microtubule cytoskeleton organization
- retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
- microtubule-based movement
- microtubule depolymerization
- mitotic spindle organization
Molecular Function
- motor activity
- microtubule motor activity
- protein binding
- ATP binding
- microtubule binding
Cellular Component
- spindle pole
- nucleus
- nucleolus
- cytoplasm
- centrosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000407818
- Coding exons
- 21
- Length
- 231088
- Individuals with no LoFs
- 125548
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 26
- Defined
- 125574
- p
- 0.000104
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 4.04 | 144 | 359 | 0.401 | 0.0000180 | 4883 |
| Missense (PolyPhen) | 28 | 139.41 | 0.20085 | 1913 | ||
| Synonymous | 1.54 | 94 | 115 | 0.817 | 0.00000547 | 1370 |
| Loss of Function | 5.48 | 2 | 38.8 | 0.0515 | 0.00000189 | 545 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0011 | notable |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000048 | 0.000046 | rare |
| European (Non-Finnish) | 0.000019 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plus end-directed microtubule-dependent motor required for normal brain development. May regulate microtubule dynamics during axonal growth. Required for normal progression through mitosis. Required for normal congress of chromosomes at the metaphase plate. Required for normal spindle dynamics during mitosis. Promotes spindle turnover. Implicated in formation of bipolar mitotic spindles. Has microtubule depolymerization activity. {ECO:0000269|PubMed:15843429, ECO:0000269|PubMed:17538014, ECO:0000269|PubMed:18411309}.;
- Disease
- DISEASE: Cortical dysplasia, complex, with other brain malformations 3 (CDCBM3) [MIM:615411]: A disorder of aberrant neuronal migration and disturbed axonal guidance. Clinical features include early-onset epilepsy, and various malformations of cortical development such as agyria, posterior or frontal pachygyria, subcortical band heterotopia, and thin corpus callosum. {ECO:0000269|PubMed:23603762}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- LoFtool
- 0.313
- RVIS EVS
- 0.26
- RVIS percentile EVS
- 70.26
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.692
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |