KIF7

protein-coding

kinesin 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

NM_198525.3

Inheritance

AR, Digenic

ClinVar variants

P:120U:852B:515

Top phenotype

Hydrolethalus syndrome 2; Acrocallosal syndrome; Joubert syndrome 12; Al-Gazali-Bakalinova syndrome

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr15:89,608,789-89,663,086

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~54.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

acrocallosal syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0008708

Submitter: Ambry Genetics

hydrolethalus syndrome 2STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013585

Submitter: Labcorp Genetics (formerly Invitae)

hydrolethalus syndrome 2MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0013585

Submitter: Genomics England PanelApp

acrocallosal syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008708

Submitter: Orphanet

hydrolethalus syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0006037

Submitter: Orphanet

acrocallosal syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008708

Submitter: PanelApp Australia

acrocallosal syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008708

Submitter: G2P

multiple epiphyseal dysplasia, Al-Gazali typeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011778

Submitter: Orphanet

acrocallosal syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008708

Submitter: Labcorp Genetics (formerly Invitae)

orofaciodigital syndrome type 6SUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010176

Submitter: Orphanet

Clinical Genomic Database (CGD)

Hydrolethalus syndrome 2; Acrocallosal syndrome; Joubert syndrome 12; Al-Gazali-Bakalinova syndromeAR/Digenic

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

Refs: 457430; 7424976; 7102724; 7166318; 3802558; 3366141; 2658584; 2729349; 2729348; 2658583; 2308155; 2051463; 1659985; 1887856; 1499582; 8092201; 8723075; 11857542; 18618999; 20301500; 21633164; 21552264; 22246503; 22587682; 23142271Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KIF7 variants in ClinVar

27 Conditions Cataloged
Acrocallosal syndromeTotal: 1447
not providedTotal: 449
Multiple epiphyseal dysplasia, Al-Gazali typeTotal: 311
Hydrolethalus syndrome 2Total: 304
not specifiedTotal: 297
Inborn genetic diseasesTotal: 286
KIF7-related disorderTotal: 112
Intellectual disabilityTotal: 13

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.

EffectPLPVUSLBBSum
synonymous
12
clinvar
452
clinvar
6
clinvar
470
missense
1
clinvar
3
clinvar
825
clinvar
53
clinvar
4
clinvar
886
nonsense
27
clinvar
25
clinvar
2
clinvar
54
start loss
1
clinvar
1
frameshift
22
clinvar
30
clinvar
10
clinvar
62
splice donor/acceptor (+/-2bp)
12
clinvar
2
clinvar
14
Total5070852505101487

Highest pathogenic variant AF is 0.00013307646

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_198525.3RefSeqNP_940927.218MANE Select
ENST00000394412.8EnsemblENSP00000377934.318MANE Select
ENST00000445906.1EnsemblENSP00000395906.12Standard
ENST00000558928.1EnsemblENSP00000504283.12Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
kif7Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.6898768201.070.00006048495
Missense (PolyPhen)319336.620.947673430
Synonymous-1.073883621.070.00002562826
Loss of Function2.024359.90.7180.00000336634

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000190.00018rare
Latino/Admixed American0.000260.00026rare
Ashkenazi Jewish0.000500.00050rare
East Asian0.000650.00065rare
Finnish0.000280.00028rare
European (Non-Finnish)0.000440.00044rare
South Asian0.000280.00026rare
Other0.000660.00065rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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