KIF2C

kinesin family member 2C, the group of Kinesins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 1:44739818-44767767

Previous symbols: [ "KNSL6" ]

Links

ENSG00000142945 ∙ NCBI:11004 ∙ OMIM:604538 ∙ HGNC:6393 ∙ Uniprot:Q99661 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF2C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF2C 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		1
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in KIF2C

This is a list of pathogenic ClinVar variants found in the KIF2C region.

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

Position	Type	Phenotype	Significance	ClinVar
1-44739982-T-C		not specified	Uncertain significance (Jan 09, 2024)
1-44747662-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-44747670-G-A		not specified	Uncertain significance (Jun 27, 2022)
1-44750462-C-T		not specified	Uncertain significance (Mar 31, 2023)
1-44750466-T-C		not specified	Uncertain significance (Dec 21, 2022)
1-44753150-C-G		not specified	Uncertain significance (Sep 22, 2023)
1-44753252-C-T		not specified	Uncertain significance (Nov 09, 2023)
1-44754787-G-A		not specified	Uncertain significance (Oct 16, 2023)
1-44755932-G-A		not specified	Uncertain significance (Dec 15, 2023)
1-44755938-C-G		not specified	Uncertain significance (Mar 29, 2023)
1-44756135-A-G		not specified	Uncertain significance (Jun 22, 2021)
1-44758087-C-T		not specified	Uncertain significance (Dec 28, 2023)
1-44758133-A-G		not specified	Uncertain significance (Dec 26, 2023)
1-44758135-G-A		not specified	Uncertain significance (Dec 21, 2022)
1-44759240-G-A		not specified	Uncertain significance (Jul 12, 2022)
1-44759314-G-A		not specified	Uncertain significance (Sep 29, 2022)
1-44760284-T-A		not specified	Uncertain significance (May 13, 2024)
1-44760431-C-G		not specified	Uncertain significance (Dec 02, 2022)
1-44760431-C-T		not specified	Uncertain significance (Apr 13, 2023)
1-44760677-T-C		not specified	Uncertain significance (Mar 28, 2024)
1-44760686-A-T		not specified	Uncertain significance (Dec 16, 2023)
1-44762363-C-T		not specified	Uncertain significance (Jun 28, 2023)
1-44762420-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-44762443-C-T		not specified	Uncertain significance (Jul 27, 2022)
1-44762444-C-T		not specified	Uncertain significance (Dec 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF2C	protein_coding	protein_coding	ENST00000372224	21	27950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000258	1.00	125307	0	441	125748	0.00176

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	335	415	0.807	0.0000231	4789
Missense in Polyphen		101	153	0.66012		1757
Synonymous	-0.574	160	151	1.06	0.00000842	1354
Loss of Function	3.90	16	43.8	0.365	0.00000240	500

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00640	0.00616
Ashkenazi Jewish	0.000706	0.000695
East Asian	0.00215	0.00207
Finnish	0.00325	0.00310
European (Non-Finnish)	0.00148	0.00143
Middle Eastern	0.00215	0.00207
South Asian	0.000263	0.000261
Other	0.00100	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In complex with KIF18B, constitutes the major microtubule plus-end depolymerizing activity in mitotic cells (PubMed:21820309). Regulates the turnover of microtubules at the kinetochore and functions in chromosome segregation during mitosis (PubMed:19060894). Plays a role in chromosome congression and is required for the lateral to end-on conversion of the chromosome- microtubule attachment (PubMed:23891108). {ECO:0000269|PubMed:19060894, ECO:0000269|PubMed:21820309, ECO:0000269|PubMed:23891108}.
• Pathway: Regulation of Microtubule Cytoskeleton;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;Aurora B signaling;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.665
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.64

Haploinsufficiency Scores

• pHI: 0.765
• hipred: Y
• hipred_score: 0.663
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.924

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kif2c

Gene ontology

• Biological process: mitotic cell cycle;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based movement;microtubule depolymerization;mitotic metaphase plate congression;cell population proliferation;antigen processing and presentation of exogenous peptide antigen via MHC class II;establishment or maintenance of microtubule cytoskeleton polarity;cell division;metaphase plate congression;attachment of mitotic spindle microtubules to kinetochore;regulation of chromosome segregation
• Cellular component: chromosome, centromeric region;kinetochore;condensed chromosome kinetochore;nucleus;centrosome;cytosol;kinesin complex;microtubule;cytoplasmic microtubule;microtubule cytoskeleton;membrane;microtubule plus-end
• Molecular function: microtubule motor activity;protein binding;ATP binding;microtubule binding;ATPase activity;centromeric DNA binding;microtubule plus-end binding