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.

• Complex cortical dysplasia with other brain malformations 3 (1 variants)
• not provided (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.

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			1	82	4	87
missense	1	3	113	22	17	156
nonsense			3	1		4
start loss			2			2
frameshift			4			4
inframe indel			1	2		3
splice donor/acceptor (+/-2bp)			2	1		3
splice region			18	26	7	51
non coding			7	121	66	194
Total	1	3	133	229	87

Variants in KIF2A

This is a list of pathogenic ClinVar variants found in the KIF2A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-62306184-G-A			Likely benign (Sep 18, 2018)
5-62306198-G-A			Likely benign (Sep 18, 2018)
5-62306211-A-C			Likely benign (Sep 18, 2018)
5-62306223-C-T			Benign (Jun 26, 2018)
5-62306392-A-G			Likely benign (Nov 25, 2018)
5-62306436-C-A		not specified	Likely benign (Oct 05, 2017)
5-62306444-G-C		not specified	Likely benign (Mar 09, 2018)
5-62306473-A-G		Complex cortical dysplasia with other brain malformations 3	Uncertain significance (Feb 11, 2022)
5-62306479-A-G			Uncertain significance (Jul 20, 2023)
5-62306480-C-T			Uncertain significance (Oct 09, 2022)
5-62306484-C-A			Likely benign (Oct 13, 2022)
5-62306491-G-A			Uncertain significance (Sep 29, 2023)
5-62306491-G-C		Microcephaly	Likely benign (Sep 01, 2022)
5-62306494-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Aug 17, 2023)
5-62306499-C-A			Likely benign (Jul 19, 2022)
5-62306499-C-G			Uncertain significance (Sep 02, 2022)
5-62306499-C-T		KIF2A-related disorder	Likely benign (May 19, 2023)
5-62306500-C-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 02, 2024)
5-62306507-G-A			Benign (Jan 15, 2024)
5-62306509-A-G			Likely benign (Jan 02, 2024)
5-62306515-G-A			Uncertain significance (Dec 07, 2020)
5-62306520-G-A		not specified	Conflicting classifications of pathogenicity (Jan 18, 2024)
5-62306542-C-T			Benign (Sep 06, 2022)
5-62306546-G-A			Likely benign (May 19, 2022)
5-62306552-AGCCCCGCTGGCCCGCTCG-A			Likely benign (Jul 07, 2023)

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