KIF22

kinesin family member 22, the group of Kinesins

Basic information

Region (hg38): 16:29790727-29805385

Previous symbols: [ "KNSL4" ]

Links

ENSG00000079616

∙ NCBI:3835 ∙ OMIM:603213 ∙ HGNC:6391 ∙ Uniprot:Q14807 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

spondyloepimetaphyseal dysplasia with multiple dislocations (Definitive), mode of inheritance: AD
spondyloepimetaphyseal dysplasia with multiple dislocations (Strong), mode of inheritance: AD
spondyloepimetaphyseal dysplasia with multiple dislocations (Supportive), mode of inheritance: AD
spondyloepimetaphyseal dysplasia with multiple dislocations (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spondyloepimetaphyseal dysplasia with joint laxity, type 2	AD	General	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	Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal	19277648; 22152677

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF22 gene.

not_provided (320 variants)
not_specified (102 variants)
Spondyloepimetaphyseal_dysplasia_with_multiple_dislocations (27 variants)
KIF22-related_disorder (11 variants)
Inborn_genetic_diseases (3 variants)
See_cases (2 variants)
Epilepsy (1 variants)
Skeletal_dysplasia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF22 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007317.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	56 clinvar	4 clinvar	63
missense	2 clinvar	6 clinvar	172 clinvar	43 clinvar	17 clinvar	240
nonsense			4 clinvar	1 clinvar		5
start loss						0
frameshift			7 clinvar	1 clinvar		8
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	2	6	189	101	21

Highest pathogenic variant AF is 0.00000371738

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF22	protein_coding	protein_coding	ENST00000160827	14	14667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.17e-10	0.977	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.141	398	406	0.980	0.0000249	4254
Missense in Polyphen		145	198.99	0.72867		2090
Synonymous	-1.82	185	156	1.18	0.00000807	1418
Loss of Function	2.24	20	34.2	0.586	0.00000200	355

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000240	0.000239
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000218	0.000217
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000184	0.000176
Middle Eastern	0.000218	0.000217
South Asian	0.000329	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Kinesin family member that is involved in spindle formation and the movements of chromosomes during mitosis and meiosis. Binds to microtubules and to DNA (By similarity). Plays a role in congression of laterally attached chromosomes in NDC80- depleted cells (PubMed:25743205). {ECO:0000250|UniProtKB:Q9I869, ECO:0000269|PubMed:25743205}.;
Disease: DISEASE: Spondyloepimetaphyseal dysplasia with joint laxity, 2 (SEMDJL2) [MIM:603546]: A bone disease characterized by short stature, distinctive midface retrusion, progressive knee malalignment (genu valgum and/or varum), generalized ligamentous laxity, and mild spinal deformity. Intellectual development is not impaired. Radiographic characteristics include significantly retarded epiphyseal ossification that evolves into epiphyseal dysplasia and precocious osteoarthritis, metaphyseal irregularities and vertical striations, constricted femoral neck, slender metacarpals and metatarsals, and mild thoracolumbar kyphosis or scoliosis with normal or mild platyspondyly. The most distinctive features for differential diagnosis of SEMDJL2 are the slender metacarpals and phalanges and the progressive degeneration of carpal bones; however, these 2 features are evident only in older children and young adults. The soft consistency of cartilage in the airways leads to laryngotracheomalacia with proneness to respiratory obstruction and inspiratory stridor in infancy and childhood. {ECO:0000269|PubMed:22152677, ECO:0000269|PubMed:22152678}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Progesterone-mediated oocyte maturation - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Kinesins;Factors involved in megakaryocyte development and platelet production;Hemostasis;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.191

Intolerance Scores

loftool: 0.800
rvis_EVS: -0.26
rvis_percentile_EVS: 34.88

Haploinsufficiency Scores

pHI: 0.141
hipred: Y
hipred_score: 0.678
ghis: 0.624

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.864

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Kif22
Phenotype: cellular phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Zebrafish Information Network

Gene name: kif22
Affected structure: post-vent region
Phenotype tag: abnormal
Phenotype quality: decreased length

Gene ontology

Biological process: mitotic cell cycle;DNA repair;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based movement;sister chromatid cohesion;mitotic metaphase plate congression;antigen processing and presentation of exogenous peptide antigen via MHC class II;metaphase plate congression
Cellular component: kinetochore;chromatin;nucleus;cytosol;kinesin complex;microtubule;nuclear speck;mitotic spindle
Molecular function: DNA binding;microtubule motor activity;protein binding;ATP binding;microtubule binding;ATPase activity