Human Gene KIF1A (ENST00000498729.9) from GENCODE V44
  Description: Homo sapiens kinesin family member 1A (KIF1A), transcript variant 6, mRNA. (from RefSeq NM_001379631)
RefSeq Summary (NM_001244008): The protein encoded by this gene is a member of the kinesin family and functions as an anterograde motor protein that transports membranous organelles along axonal microtubules. Mutations at this locus have been associated with spastic paraplegia-30 and hereditary sensory neuropathy IIC. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Apr 2012]. ##RefSeq-Attributes-START## RefSeq Select criteria :: based on manual assertion, conservation ##RefSeq-Attributes-END##
Gencode Transcript: ENST00000498729.9
Gencode Gene: ENSG00000130294.18
Transcript (Including UTRs)
   Position: hg38 chr2:240,713,767-240,820,219 Size: 106,453 Total Exon Count: 49 Strand: -
Coding Region
   Position: hg38 chr2:240,717,364-240,797,752 Size: 80,389 Coding Exon Count: 48 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:240,713,767-240,820,219)mRNA (may differ from genome)Protein (1791 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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ReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Kinesin-like protein KIF1A; AltName: Full=Axonal transporter of synaptic vesicles; AltName: Full=Microtubule-based motor KIF1A; AltName: Full=Unc-104- and KIF1A-related protein; Short=hUnc-104;
FUNCTION: Motor for anterograde axonal transport of synaptic vesicle precursors (By similarity).
SUBUNIT: Monomer. Interacts with PPFIA1 and PPFIA4 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. Note=Expressed in distal regions of neurites.
TISSUE SPECIFICITY: Expressed in neurons.
DISEASE: Defects in KIF1A are the cause of spastic paraplegia autosomal recessive type 30 (SPG30) [MIM:610357]. SPG30 is a form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. SPG30 is characterized by onset in the first or second decades of unsteady spastic gait and hyperreflexia of the lower limbs.
DISEASE: Defects in KIF1A are the cause of hereditary sensory neuropathy type 2C (HSN2C) [MIM:614213]. HSN2C is a neurodegenerative disorder characterized by onset in the first decade of progressive distal sensory loss leading to ulceration and amputation of the fingers and toes. Affected individuals also develop distal muscle weakness, primarily affecting the lower limbs.
DISEASE: Defects in KIF1A are the cause of mental retardation autosomal dominant type 9 (MRD9) [MIM:614255]. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period.
SIMILARITY: Belongs to the kinesin-like protein family. Unc-104 subfamily.
SIMILARITY: Contains 1 FHA domain.
SIMILARITY: Contains 1 kinesin-motor domain.
SIMILARITY: Contains 1 PH domain.
SEQUENCE CAUTION: Sequence=AAB97363.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAE06111.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAE06111.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact leading to C-terminal exon with non-canonical splice junction;

-  Primer design for this transcript

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: KIF1A
Diseases sorted by gene-association score: spastic paraplegia 30, autosomal recessive* (1298), neuropathy, hereditary sensory, type iic* (900), peho syndrome* (543), hereditary sensory and autonomic neuropathy type iic* (500), neuropathy, hereditary sensory and autonomic, type ii* (433), hereditary spastic paraplegia* (415), troyer syndrome* (283), neuropathy, hereditary sensory, with spastic paraplegia* (231), spastic paraplegia 7, autosomal recessive* (231), infantile-onset ascending hereditary spastic paralysis* (231), spastic paraplegia 30* (151), autosomal dominant non-syndromic intellectual disability* (101), paraplegia (19), spasticity (12), adrenal neuroblastoma (7), charcot-marie-tooth disease, axonal, type 2k (6), shprintzen-goldberg syndrome (6), spastic paraparesis (5), neuropathy (5), insensitivity to pain, congenital (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 179.34 RPKM in Brain - Cortex
Total median expression: 1629.83 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -63.60158-0.403 Picture PostScript Text
3' UTR -1592.003597-0.443 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000253 - FHA_dom
IPR022140 - KIF1B
IPR022164 - Kinesin-like
IPR019821 - Kinesin_motor_CS
IPR001752 - Kinesin_motor_dom
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology
IPR008984 - SMAD_FHA_domain

Pfam Domains:
PF12473 - Kinesin protein
PF00498 - FHA domain
PF12423 - Kinesin protein 1B
PF00225 - Kinesin motor domain
PF00169 - PH domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
4EGX - X-ray MuPIT 4EJQ - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q12756
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI Ensembl   
Protein Sequence Protein Sequence   
Alignment Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003774 motor activity
GO:0003777 microtubule motor activity
GO:0005524 ATP binding
GO:0008017 microtubule binding
GO:0016887 ATPase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0007018 microtubule-based movement
GO:0008089 anterograde axonal transport
GO:0022027 interkinetic nuclear migration
GO:0098840 protein transport along microtubule
GO:1990048 anterograde neuronal dense core vesicle transport
GO:1990049 retrograde neuronal dense core vesicle transport

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005871 kinesin complex
GO:0005874 microtubule
GO:0008021 synaptic vesicle
GO:0030424 axon
GO:0030425 dendrite
GO:0032991 macromolecular complex
GO:0043025 neuronal cell body
GO:0098793 presynapse
GO:0098794 postsynapse
GO:1904115 axon cytoplasm

-  Descriptions from all associated GenBank mRNAs
  AB290172 - Homo sapiens mRNA for KIF1A variant protein, complete cds.
AB210029 - Homo sapiens mRNA for KIF1A variant protein, partial cds, clone: hh05223.
X90840 - H.sapiens mRNA for axonal transporter of synaptic vesicles.
AK307119 - Homo sapiens cDNA, FLJ97067.
BC111780 - Homo sapiens kinesin family member 1A, mRNA (cDNA clone MGC:133286 IMAGE:40037563), complete cds.
BC111799 - Homo sapiens kinesin family member 1A, mRNA (cDNA clone MGC:133285 IMAGE:40037561), complete cds.
AB384678 - Synthetic construct DNA, clone: pF1KB0051, Homo sapiens KIF1A gene for kinesin family member 1A, complete cds, without stop codon, in Flexi system.
AB587531 - Synthetic construct DNA, clone: pF1KE0700, Homo sapiens KIF1A gene for kinesin family member 1A, without stop codon, in Flexi system.
KJ534874 - Homo sapiens clone KIF1A_iso-B_adult-A14 kinesin family member 1A isoform B (KIF1A) mRNA, partial cds, alternatively spliced.
KJ534875 - Homo sapiens clone KIF1A_iso-A_fetal-F13 kinesin family member 1A isoform A (KIF1A) mRNA, partial cds, alternatively spliced.
KJ534994 - Homo sapiens clone KIF1A_iso-D_fetal-F03 kinesin family member 1A isoform D (KIF1A) mRNA, complete cds, alternatively spliced.
KJ535053 - Homo sapiens clone KIF1A_iso-C_fetal-F05 kinesin family member 1A isoform C (KIF1A) mRNA, complete cds, alternatively spliced.
BX537556 - Homo sapiens mRNA; cDNA DKFZp686N1746 (from clone DKFZp686N1746).
BX649015 - Homo sapiens mRNA; cDNA DKFZp686I2094 (from clone DKFZp686I2094).
AB209138 - Homo sapiens mRNA for axonal transport of synaptic vesicles variant protein.
BC021199 - Homo sapiens kinesin family member 1A, mRNA (cDNA clone IMAGE:3944595).
BC009491 - Homo sapiens cDNA clone IMAGE:3936963.
AK054791 - Homo sapiens cDNA FLJ30229 fis, clone BRACE2001892.
JD498396 - Sequence 479420 from Patent EP1572962.
JD559547 - Sequence 540571 from Patent EP1572962.
JD415888 - Sequence 396912 from Patent EP1572962.
JD098497 - Sequence 79521 from Patent EP1572962.
JD440462 - Sequence 421486 from Patent EP1572962.
JD457969 - Sequence 438993 from Patent EP1572962.
JD484258 - Sequence 465282 from Patent EP1572962.
JD565747 - Sequence 546771 from Patent EP1572962.
JD148440 - Sequence 129464 from Patent EP1572962.
JD021675 - Sequence 2699 from Patent EP1572962.
JD034280 - Sequence 15304 from Patent EP1572962.
JD162227 - Sequence 143251 from Patent EP1572962.
JD363710 - Sequence 344734 from Patent EP1572962.
JD422149 - Sequence 403173 from Patent EP1572962.
JD334735 - Sequence 315759 from Patent EP1572962.
JD340571 - Sequence 321595 from Patent EP1572962.
JD189107 - Sequence 170131 from Patent EP1572962.
JD146056 - Sequence 127080 from Patent EP1572962.
JD542454 - Sequence 523478 from Patent EP1572962.
JD234631 - Sequence 215655 from Patent EP1572962.
JD540237 - Sequence 521261 from Patent EP1572962.
JD310339 - Sequence 291363 from Patent EP1572962.
JD062464 - Sequence 43488 from Patent EP1572962.
JD545071 - Sequence 526095 from Patent EP1572962.
JD020565 - Sequence 1589 from Patent EP1572962.
JD023045 - Sequence 4069 from Patent EP1572962.
JD029689 - Sequence 10713 from Patent EP1572962.
JD022834 - Sequence 3858 from Patent EP1572962.
JD022835 - Sequence 3859 from Patent EP1572962.
JD033774 - Sequence 14798 from Patent EP1572962.
JD338986 - Sequence 320010 from Patent EP1572962.
JD187849 - Sequence 168873 from Patent EP1572962.
JD422851 - Sequence 403875 from Patent EP1572962.
JD140818 - Sequence 121842 from Patent EP1572962.
JD462066 - Sequence 443090 from Patent EP1572962.
JD231077 - Sequence 212101 from Patent EP1572962.
JD525393 - Sequence 506417 from Patent EP1572962.
JD170321 - Sequence 151345 from Patent EP1572962.
JD390936 - Sequence 371960 from Patent EP1572962.
JD253664 - Sequence 234688 from Patent EP1572962.
JD464921 - Sequence 445945 from Patent EP1572962.
JD479803 - Sequence 460827 from Patent EP1572962.
DQ579144 - Homo sapiens piRNA piR-47256, complete sequence.
JD347199 - Sequence 328223 from Patent EP1572962.
JD449509 - Sequence 430533 from Patent EP1572962.
JD279628 - Sequence 260652 from Patent EP1572962.
JD368110 - Sequence 349134 from Patent EP1572962.
JD370174 - Sequence 351198 from Patent EP1572962.
JD498211 - Sequence 479235 from Patent EP1572962.
JD365339 - Sequence 346363 from Patent EP1572962.
JD563569 - Sequence 544593 from Patent EP1572962.
JD527247 - Sequence 508271 from Patent EP1572962.
JD349248 - Sequence 330272 from Patent EP1572962.
JD487250 - Sequence 468274 from Patent EP1572962.
JD483135 - Sequence 464159 from Patent EP1572962.
JD229502 - Sequence 210526 from Patent EP1572962.
JD343168 - Sequence 324192 from Patent EP1572962.
JD408709 - Sequence 389733 from Patent EP1572962.
JD135001 - Sequence 116025 from Patent EP1572962.
JD467242 - Sequence 448266 from Patent EP1572962.
JD054085 - Sequence 35109 from Patent EP1572962.
JD329743 - Sequence 310767 from Patent EP1572962.
JD348240 - Sequence 329264 from Patent EP1572962.
JD042670 - Sequence 23694 from Patent EP1572962.
JD348254 - Sequence 329278 from Patent EP1572962.
JD279329 - Sequence 260353 from Patent EP1572962.
JD423161 - Sequence 404185 from Patent EP1572962.
JD403203 - Sequence 384227 from Patent EP1572962.
JD242057 - Sequence 223081 from Patent EP1572962.
JD148850 - Sequence 129874 from Patent EP1572962.
AF038173 - Homo sapiens clone 23723 axonal transporter of synaptic vesicles (ATSV) mRNA, partial cds.
AF052089 - Homo sapiens clone 23630 and 23737 mRNA sequences.
AK297530 - Homo sapiens cDNA FLJ61319 complete cds, highly similar to Kinesin-like protein KIF1A.
L79946 - Homo sapiens clone 25553 unknown (HUNC-104) mRNA, partial cds.
AK130880 - Homo sapiens cDNA FLJ27370 fis, clone UBA03786, highly similar to Kinesin-like protein KIF1A.
JD282363 - Sequence 263387 from Patent EP1572962.
JD556705 - Sequence 537729 from Patent EP1572962.
JD116454 - Sequence 97478 from Patent EP1572962.
JD132750 - Sequence 113774 from Patent EP1572962.
JD475072 - Sequence 456096 from Patent EP1572962.
JD416463 - Sequence 397487 from Patent EP1572962.
U37194 - Human UNC-104- and KIF1A-related protein mRNA, partial cds.
DQ575219 - Homo sapiens piRNA piR-43331, complete sequence.
MN897723 - Homo sapiens kinesin family member 1A (KIF1A) mRNA, partial cds.
BC064906 - Homo sapiens kinesin family member 1A, mRNA (cDNA clone IMAGE:6025756), partial cds.
AF004425 - Homo sapiens microtubule-based motor (HsKIF1A) mRNA, partial cds.
AB621817 - Homo sapiens KIF1A mRNA for kinesin-like protein KIF1A, partial cds, clone: HP07897-RBdS014C08.
JD320736 - Sequence 301760 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q12756 (Reactome details) participates in the following event(s):

R-HSA-983266 Kinesins bind microtubules
R-HSA-6811426 Retrograde COPI vesicles bind kinesin and microtubules
R-HSA-6811423 Retrograde vesicle is tethered at the ER by the NRZ complex and t-SNAREs
R-HSA-983189 Kinesins
R-HSA-6811434 COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-983231 Factors involved in megakaryocyte development and platelet production
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-109582 Hemostasis
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ATSV, C2orf20, ENST00000498729.1, ENST00000498729.2, ENST00000498729.3, ENST00000498729.4, ENST00000498729.5, ENST00000498729.6, ENST00000498729.7, ENST00000498729.8, KIF1A_HUMAN, NM_001379631, O95068, Q12756, Q13355, Q14752, Q2NKJ6, Q4LE42, Q53T78, Q59GH1, Q63Z40, Q6P1R9, Q7KZ57, uc010fzk.1, uc010fzk.2, uc010fzk.3, uc010fzk.4, uc010fzk.5
UCSC ID: ENST00000498729.9
RefSeq Accession: NM_001244008
Protein: Q12756 (aka KIF1A_HUMAN or KF1A_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene KIF1A:
hsan2 (Hereditary Sensory and Autonomic Neuropathy Type II)
hsp (Hereditary Spastic Paraplegia Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.