KIF2A

kinesin family member 2A, the group of Kinesins

Basic information

Region (hg38): 5:62306162-62391025

Previous symbols: [ "KIF2" ]

Links

ENSG00000068796

∙ NCBI:3796 ∙ OMIM:602591 ∙ HGNC:6318 ∙ Uniprot:O00139 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

complex cortical dysplasia with other brain malformations 3 (Moderate), mode of inheritance: AD
complex cortical dysplasia with other brain malformations 3 (Strong), mode of inheritance: AD
complex cortical dysplasia with other brain malformations 3 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cortical dysplasia, complex, with other brain malformations 3	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	Neurologic	23603762

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF2A gene.

not_provided (507 variants)
Inborn_genetic_diseases (29 variants)
Complex_cortical_dysplasia_with_other_brain_malformations_3 (23 variants)
not_specified (21 variants)
KIF2A-related_disorder (12 variants)
Abnormal_cerebral_morphology (1 variants)
Microcephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_001098511.3. 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			5 clinvar	94 clinvar	5 clinvar	104
missense	2 clinvar	4 clinvar	159 clinvar	35 clinvar	11 clinvar	211
nonsense	1 clinvar		3 clinvar	1 clinvar		5
start loss			1			1
frameshift			4 clinvar	1 clinvar		5
splice donor/acceptor (+/-2bp)			2 clinvar	2 clinvar		4
Total	3	4	174	133	16

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF2A	protein_coding	protein_coding	ENST00000407818	21	231088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000238	125548	0	26	125574	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.04	144	359	0.401	0.0000180	4883
Missense in Polyphen		28	139.41	0.20085		1913
Synonymous	1.54	94	115	0.817	0.00000547	1370
Loss of Function	5.48	2	38.8	0.0515	0.00000189	545

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00133	0.00126
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000477	0.0000462
European (Non-Finnish)	0.0000186	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Plus end-directed microtubule-dependent motor required for normal brain development. May regulate microtubule dynamics during axonal growth. Required for normal progression through mitosis. Required for normal congress of chromosomes at the metaphase plate. Required for normal spindle dynamics during mitosis. Promotes spindle turnover. Implicated in formation of bipolar mitotic spindles. Has microtubule depolymerization activity. {ECO:0000269|PubMed:15843429, ECO:0000269|PubMed:17538014, ECO:0000269|PubMed:18411309}.;
Disease: DISEASE: Cortical dysplasia, complex, with other brain malformations 3 (CDCBM3) [MIM:615411]: A disorder of aberrant neuronal migration and disturbed axonal guidance. Clinical features include early-onset epilepsy, and various malformations of cortical development such as agyria, posterior or frontal pachygyria, subcortical band heterotopia, and thin corpus callosum. {ECO:0000269|PubMed:23603762}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Kinesins;Factors involved in megakaryocyte development and platelet production;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Hemostasis;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;PLK1 signaling events;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.126

Intolerance Scores

loftool: 0.313
rvis_EVS: 0.26
rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

pHI: 0.181
hipred: Y
hipred_score: 0.825
ghis: 0.584

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.692

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Kif2a
Phenotype: cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);

Gene ontology

Biological process: microtubule cytoskeleton organization;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based movement;microtubule depolymerization;mitotic spindle organization;nervous system development;antigen processing and presentation of exogenous peptide antigen via MHC class II;cell differentiation;regulation of cell migration;cell division;mitotic spindle assembly
Cellular component: spindle pole;nucleus;nucleolus;cytoplasm;centrosome;centriole;cytosol;kinesin complex;microtubule;spindle microtubule;membrane;nuclear body;sperm principal piece;centriolar subdistal appendage
Molecular function: motor activity;microtubule motor activity;protein binding;ATP binding;microtubule binding;ATPase activity