KIF7
protein-codingkinesin family member 7, the group of Kinesins
Gene summary
This gene encodes a cilia-associated protein belonging to the kinesin family. This protein plays a role in the sonic hedgehog (SHH) signaling pathway through the regulation of GLI transcription factors. It functions as a negative regulator of the SHH pathway by preventing inappropriate activation of GLI2 in the absence of ligand, and as a positive regulator by preventing the processing of GLI3 into its repressor form. Mutations in this gene have been associated with various ciliopathies. [provided by RefSeq, Oct 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~54.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0008708
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0013585
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0013585
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0008708
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0006037
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0008708
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0008708
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0011778
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0008708
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0010176
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Gastrointestinal; Musculoskeletal; Neurologic; Renal; Ophthalmologic
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
Comments: The condition may involve multi-systemic manifestations, including sequelae affecting the renal and hepatic systems, and surveillance and avoidance of certain medications (eg, nephrotoxic agents) may be beneficial; Digenic inheritance (with CEP41) has been reported
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KIF7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198525.3. 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 | 12 | 452 | 6 | 470 | ||
| missense | 1 | 3 | 825 | 53 | 4 | 886 |
| nonsense | 27 | 25 | 2 | 54 | ||
| start loss | 1 | 1 | ||||
| frameshift | 22 | 30 | 10 | 62 | ||
| splice donor/acceptor (+/-2bp) | 12 | 2 | 14 | |||
| Total | 50 | 70 | 852 | 505 | 10 | 1487 |
Highest pathogenic variant AF is 0.00013307646
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_940927.2 | 18 | MANE Select | |
| Ensembl | ENSP00000377934.3 | 18 | MANE Select | |
| Ensembl | ENSP00000395906.1 | 2 | Standard | |
| Ensembl | ENSP00000504283.1 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| kif7 | Danio rerio | Structure: slow muscle cell Quality: increased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Basal cell carcinoma - Homo sapiens (human)
- Pathways in cancer - Homo sapiens (human)
- Hedgehog signaling pathway - Homo sapiens (human)
- Hedgehog Signaling Pathway
- Hedgehog Signaling Pathway
Biological Process
- microtubule-based movement
- negative regulation of smoothened signaling pathway
- positive regulation of smoothened signaling pathway
Molecular Function
- microtubule motor activity
- protein binding
- ATP binding
- microtubule binding
- ATPase activity
Cellular Component
- cytoplasm
- kinesin complex
- microtubule
- cilium
- ciliary basal body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000394412
- Coding exons
- 18
- Length
- 46663
- Individuals with no LoFs
- 125651
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 97
- Defined
- 125748
- p
- 0.000386
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.689 | 876 | 820 | 1.07 | 0.0000604 | 8495 |
| Missense (PolyPhen) | 319 | 336.62 | 0.94767 | 3430 | ||
| Synonymous | -1.07 | 388 | 362 | 1.07 | 0.0000256 | 2826 |
| Loss of Function | 2.02 | 43 | 59.9 | 0.718 | 0.00000336 | 634 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.00050 | 0.00050 | rare |
| East Asian | 0.00065 | 0.00065 | rare |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.00044 | 0.00044 | rare |
| South Asian | 0.00028 | 0.00026 | rare |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Essential for hedgehog signaling regulation: acts as both a negative and positive regulator of sonic hedgehog (Shh) and Indian hedgehog (Ihh) pathways, acting downstream of SMO, through both SUFU-dependent and -independent mechanisms (PubMed:21633164). Involved in the regulation of microtubular dynamics. Required for proper organization of the ciliary tip and control of ciliary localization of SUFU-GLI2 complexes (By similarity). Required for localization of GLI3 to cilia in response to Shh. Negatively regulates Shh signaling by preventing inappropriate activation of the transcriptional activator GLI2 in the absence of ligand. Positively regulates Shh signaling by preventing the processing of the transcription factor GLI3 into its repressor form. In keratinocytes, promotes the dissociation of SUFU-GLI2 complexes, GLI2 nuclear translocation and Shh signaling activation (By similarity). Involved in the regulation of epidermal differentiation and chondrocyte development (By similarity). {ECO:0000250|UniProtKB:B7ZNG0, ECO:0000269|PubMed:21633164}.;
- Disease
- DISEASE: Note=Ciliary dysfunction leads to a broad spectrum of disorders, collectively termed ciliopathies. The ciliopathy range of diseases includes Meckel-Gruber syndrome, Bardet-Biedl syndrome, Joubert syndrome, and hydrolethalus syndrome among others. Single-locus allelism is insufficient to explain the variable penetrance and expressivity of such disorders, leading to the suggestion that variations across multiple sites of the ciliary proteome influence the clinical outcome. Primary ciliopathy loci can be modulated by pathogenic lesions in other ciliary genes to either exacerbate overall severity or induce specific endophenotypes. KIF7 may be causally associated with diverse ciliopathies, and also acts as a modifier gene across the ciliopathy spectrum.; DISEASE: Bardet-Biedl syndrome (BBS) [MIM:209900]: A syndrome characterized by usually severe pigmentary retinopathy, early- onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:21552264}. Note=The gene represented in this entry may act as a disease modifier. Heterozygous missense mutations in KIF7 may genetically interact with other BBS genes and contribute to disease manifestation and severity.; DISEASE: Hydrolethalus syndrome 2 (HLS2) [MIM:614120]: An embryonic lethal disorder characterized by hydrocephaly or anencephaly, postaxial polydactyly of the upper limbs, and pre- or postaxial polydactyly of the lower limbs. Duplication of the hallux is a common finding. {ECO:0000269|PubMed:21552264}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Acrocallosal syndrome (ACLS) [MIM:200990]: An autosomal recessive syndrome characterized by hypogenesis or agenesis of the corpus callosum. Clinical features include postaxial polydactyly, hallux duplication, macrocephaly, craniofacial abnormalities, severe developmental delay and mental retardation. {ECO:0000269|PubMed:21552264, ECO:0000269|PubMed:23125460, ECO:0000269|PubMed:26174511}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Joubert syndrome 12 (JBTS12) [MIM:200990]: A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease. {ECO:0000269|PubMed:21633164}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Al-Gazali-Bakalinova syndrome (AGBK) [MIM:607131]: An autosomal recessive syndrome consisting of macrocephaly, multiple epiphyseal dysplasia and distinctive facial appearance. {ECO:0000269|PubMed:22587682}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- LoFtool
- 0.786
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 33.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.672
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |