KIF6
protein-codingkinesin family member 6, the group of Kinesins
Gene summary
This gene encodes a member of a family of molecular motors which are involved in intracellular transport of protein complexes, membrane organelles, and messenger ribonucleic acid along microtubules. Kinesins function as homodimeric molecules with two N-terminal head domains that move along microtubules and two C-terminal tail domains that interact with the transported cargo, either directly or indirectly, through adapter molecules. This gene is ubiquitously expressed in coronary arteries and other vascular tissue. A naturally occurring mutation in this gene is associated with coronary heart disease. [provided by RefSeq, May 2017]
- C6orf102
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~395.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0100038
Submitter: LiferaOmics
Genetic evidence – Published PMID: 30475797 – Reports one consanguineous family with a neurodevelopmental disorder characterized by global developmental delay/intellectual disability, macrocephaly, hypotonia, and EEG abnormalities, harboring a homozygous truncating frameshift variant in KIF6 (c.1193delT; p.Leu398Glnfs*2). Parents were first cousins and confirmed heterozygous carriers; an unaffected sibling was also heterozygous. Phenotype is consistent with an autosomal recessive neurodevelopmental disorder. Case-level (biallelic predicted null in AR model; homozygous scored once; consanguineous so −0.5 applied) = (1.5 − 0.5) = 1.0; segregation (parental carrier confirmation; one additional heterozygous unaffected sibling; conservative) = 0.5; case-control = 0; PMID: 30475797 total = 1.5. Published genetic evidence total = 1.5/12 Genetic evidence – Our cases Family 1 – One proband. Case-level (biallelic predicted null in AR model; homozygous scored once; consanguinity −0.5) = (1.5 − 0.5) = 1.0; segregation = 0; case-control = 0; Family 1 total = 1.0. Family 2 – One proband. Case-level (biallelic predicted null in AR model; homozygous scored once; consanguinity unknown so no deduction applied) = 1.5;segregation = 0; case-control = 0; Family 2 total = 1.5. Our cases total = (1.0 + 1.5) = 2.5/12 Total genetic evidence (published + our cases) 1.5 + 2.5 = 4.0/12 Experimental evidence – Published PMID: 30475797 – Functional studies demonstrate that KIF6 loss-of-function disrupts ependymal cilia structure and cerebrospinal fluid dynamics. A mouse model harboring a C-terminal truncating mutation developed progressive hydrocephalus with ependymal cilia defects; zebrafish models showed ventricular dilation and reduced cilia. These findings support a loss-of-function mechanism consistent with neurodevelopmental pathology. Model systems evidence (Expression and vertebrate models recapitulating relevant neurological phenotype) = 2.5; experimental total = 2.5. Experimental evidence total = 2.5/6 Overall score Overall score = 4.0 + 2.5 = 6.5/18
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KIF6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_145027.6. 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 | 1 | 1 | ||||
| missense | 119 | 3 | 122 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 1 | 125 | 4 | 0 | 130 |
Highest pathogenic variant AF is 0.00009479096
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_659464.3 | 23 | MANE Select | |
| Ensembl | ENSP00000287152.7 | 23 | MANE Select | |
| RefSeq | NP_001275949.1 | 22 | Standard | |
| RefSeq | NP_001275950.1 | 22 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| kif6 | Danio rerio | Structure: vertebral column Quality: curved abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Kinesins
- Factors involved in megakaryocyte development and platelet production
- Hemostasis
Biological Process
- microtubule-based movement
Molecular Function
- microtubule motor activity
- protein binding
- ATP binding
- microtubule binding
- ATPase activity
Cellular Component
- male germ cell nucleus
- cytoplasm
- kinesin complex
- microtubule
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000287152
- Coding exons
- 23
- Length
- 395416
- Individuals with no LoFs
- 125583
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 165
- Defined
- 125748
- p
- 0.000656
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.434 | 408 | 433 | 0.941 | 0.0000223 | 5371 |
| Missense (PolyPhen) | 158 | 151.02 | 1.0462 | 1891 | ||
| Synonymous | 1.21 | 139 | 158 | 0.878 | 0.00000841 | 1475 |
| Loss of Function | 0.927 | 45 | 52.2 | 0.862 | 0.00000296 | 599 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00086 | 0.00086 | rare |
| Latino/Admixed American | 0.00067 | 0.00067 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00077 | 0.00076 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00087 | 0.00086 | rare |
| South Asian | 0.00040 | 0.00039 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0948
Intolerance Scores
- LoFtool
- 0.890
- RVIS EVS
- 0.3
- RVIS percentile EVS
- 71.64
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.677
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |