KIF11

kinesin family member 11, the group of Kinesins

Basic information

Region (hg38): 10:92574104-92655395

Previous symbols: [ "KNSL1" ]

Links

ENSG00000138160 ∙ NCBI:3832 ∙ OMIM:148760 ∙ HGNC:6388 ∙ Uniprot:P52732 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (Definitive), mode of inheritance: AD
• microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (Strong), mode of inheritance: AD
• microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (Strong), mode of inheritance: AD
• microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (Supportive), mode of inheritance: AD
• microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly with or without chorioretinopathy, lymphedema, or impaired intellectual development	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	Cardiovascular; Craniofacial; Neurologic; Ophthalmologic	15930898; 22653704; 22284827; 25115524

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF11 gene.

• not provided (663 variants)
• Microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability (75 variants)
• not specified (32 variants)
• Inborn genetic diseases (20 variants)
• KIF11-related condition (6 variants)
• Retinal dystrophy (4 variants)
• Neutropenia;Lymphopenia (2 variants)
• Microcephaly and chorioretinopathy 1 (1 variants)
• Retinitis pigmentosa (1 variants)
• Developmental disorder (1 variants)
• Neurodevelopmental disorder (1 variants)
• Microcephaly (1 variants)
• Neurodevelopmental delay (1 variants)
• Intellectual disability (1 variants)
• Intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome (1 variants)
• Microcephaly with or without chorioretinopathy, lymphedema or intellectual disability (MCLID) (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF11 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	120	8	131
missense		4	197	28	6	235
nonsense	22	7				29
start loss	2	1				3
frameshift	46	14	1			61
inframe indel		2	6			8
splice donor/acceptor (+/-2bp)	10	9				19
splice region	1	2	24	28	3	58
non coding			5	98	77	180
Total	80	37	212	246	91

Variants in KIF11

This is a list of pathogenic ClinVar variants found in the KIF11 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-92592748-A-T			Benign (Jul 08, 2018)
10-92592861-C-T			Benign (Jul 08, 2018)
10-92592979-A-G			Benign (Jul 31, 2018)
10-92592990-C-G			Likely benign (Mar 17, 2019)
10-92593066-C-G			Benign (Jul 31, 2018)
10-92593161-A-G			Benign (Jul 08, 2018)
10-92593375-CAT-AA		Microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability	Pathogenic (Sep 24, 2015)
10-92593376-A-G		Microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability	Pathogenic (Jul 14, 2023)
10-92593377-T-C			Pathogenic (Dec 04, 2017)
10-92593380-C-T			Uncertain significance (May 12, 2022)
10-92593384-G-A			Likely benign (Dec 09, 2023)
10-92593399-TGC-AG			Pathogenic (Dec 23, 2015)
10-92593401-C-G			Uncertain significance (Sep 08, 2023)
10-92593405-G-A			Likely benign (Jun 15, 2022)
10-92593416-A-C			Likely benign (Sep 13, 2022)
10-92593420-G-A			Likely benign (Oct 03, 2022)
10-92593444-G-C			Likely benign (Jan 13, 2022)
10-92593451-A-G			Pathogenic/Likely pathogenic (Jul 07, 2022)
10-92593452-G-T			Uncertain significance (Jun 01, 2018)
10-92593453-G-A		Microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability	Pathogenic (May 02, 2023)
10-92593457-G-C		not specified • Neutropenia;Lymphopenia • KIF11-related disorder	Benign/Likely benign (Jan 22, 2024)
10-92593459-A-C			Likely benign (Sep 22, 2022)
10-92593459-AGAG-A		not specified • KIF11-related disorder	Benign/Likely benign (Nov 27, 2023)
10-92593463-G-A			Likely benign (Mar 24, 2023)
10-92593470-A-G			Likely benign (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF11	protein_coding	protein_coding	ENST00000260731	22	62108

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.66e-7	125711	0	6	125717	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.27	310	520	0.596	0.0000257	6946
Missense in Polyphen		41	162.32	0.25258		1997
Synonymous	0.623	172	183	0.941	0.00000845	1980
Loss of Function	6.43	2	52.1	0.0384	0.00000268	697

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000128	0.0000992
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000281	0.0000264
Middle Eastern	0.000110	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Motor protein required for establishing a bipolar spindle during mitosis (PubMed:19001501). Required in non-mitotic cells for transport of secretory proteins from the Golgi complex to the cell surface (PubMed:23857769). {ECO:0000269|PubMed:19001501, ECO:0000269|PubMed:23857769}.
• Disease: DISEASE: Microcephaly with or without chorioretinopathy, lymphedema, or mental retardation (MCLMR) [MIM:152950]: An autosomal dominant disorder that involves an overlapping but variable spectrum of central nervous system and ocular developmental anomalies. Microcephaly ranges from mild to severe and is often associated with mild to moderate developmental delay and a characteristic facial phenotype with upslanting palpebral fissures, broad nose with rounded tip, long philtrum with thin upper lip, prominent chin, and prominent ears. Chorioretinopathy is the most common eye abnormality, but retinal folds, microphthalmia, and myopic and hypermetropic astigmatism have also been reported, and some individuals have no overt ocular phenotype. Congenital lymphedema, when present, is typically confined to the dorsa of the feet, and lymphoscintigraphy reveals the absence of radioactive isotope uptake from the webspaces between the toes. {ECO:0000269|PubMed:22284827}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: 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: 0.134

Intolerance Scores

• loftool: 0.0258
• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.176
• hipred: Y
• hipred_score: 0.831
• ghis: 0.612

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.784

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kif11
• Phenotype: embryo phenotype; reproductive system 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); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: kif11
• Affected structure: radial glial cell
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: mitotic cell cycle;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based movement;spindle organization;mitotic spindle organization;mitotic centrosome separation;antigen processing and presentation of exogenous peptide antigen via MHC class II;regulation of mitotic centrosome separation;cell division;mitotic spindle assembly
• Cellular component: spindle pole;nucleus;spindle;cytosol;kinesin complex;microtubule;spindle microtubule;membrane;protein-containing complex;mitotic spindle
• Molecular function: microtubule motor activity;ATP binding;microtubule binding;ATP-dependent microtubule motor activity, plus-end-directed;ATPase activity;protein kinase binding