KIF6

protein-coding

kinesin 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]

Previous symbols:
  • C6orf102

MANE transcript

NM_145027.6

Inheritance

AR

ClinVar variants

P:1U:125B:4

Top phenotype

KIF6-related disorder

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr6:39,329,990-39,725,408

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~395.4 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

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

4 Conditions Cataloged
not specifiedTotal: 115
not providedTotal: 6
KIF6-related disorderTotal: 2
Primary ciliary dyskinesiaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
119
clinvar
3
clinvar
122
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
5
clinvar
5
Total0112540130

Highest pathogenic variant AF is 0.00009479096

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_145027.6RefSeqNP_659464.323MANE Select
ENST00000287152.12EnsemblENSP00000287152.723MANE Select
NM_001289020.3RefSeqNP_001275949.122Standard
NM_001289021.3RefSeqNP_001275950.122Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
kif6Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4344084330.9410.00002235371
Missense (PolyPhen)158151.021.04621891
Synonymous1.211391580.8780.000008411475
Loss of Function0.9274552.20.8620.00000296599

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000860.00086rare
Latino/Admixed American0.000670.00067rare
Ashkenazi Jewish00.0absent
East Asian0.000770.00076rare
Finnish0.000140.00014rare
European (Non-Finnish)0.000870.00086rare
South Asian0.000400.00039rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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