KIF20A

kinesin family member 20A, the group of Kinesins

Basic information

Region (hg38): 5:138178719-138187723

Previous symbols: [ "RAB6KIFL" ]

Links

ENSG00000112984 ∙ NCBI:10112 ∙ OMIM:605664 ∙ HGNC:9787 ∙ Uniprot:O95235 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial isolated restrictive cardiomyopathy (Supportive), mode of inheritance: AD
• cardiomyopathy, familial restrictive, 6 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cardiomyopathy, familial restrictive, 6	AR	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	29357359

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF20A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF20A 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	62	7	72
missense			217	5	3	225
nonsense			9			9
start loss			1			1
frameshift			4			4
inframe indel			2			2
splice donor/acceptor (+/-2bp)			6			6
splice region			13	11	3	27
non coding				62	4	66
Total	0	0	242	129	14

Variants in KIF20A

This is a list of pathogenic ClinVar variants found in the KIF20A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-138179681-A-G			Uncertain significance (May 01, 2023)
5-138179684-T-G			Uncertain significance (Jun 19, 2023)
5-138179686-G-T			Likely benign (Sep 11, 2023)
5-138179690-G-C			Uncertain significance (Nov 23, 2022)
5-138179692-G-T			Likely benign (Dec 07, 2022)
5-138179703-C-T		not specified	Uncertain significance (Jul 14, 2024)
5-138179704-G-A			Benign (Dec 13, 2023)
5-138179704-G-C			Benign (Nov 10, 2023)
5-138179710-G-A			Uncertain significance (May 22, 2023)
5-138179718-T-C			Uncertain significance (Dec 04, 2023)
5-138179770-T-G			Uncertain significance (Feb 25, 2022)
5-138179786-C-T			Uncertain significance (Sep 05, 2022)
5-138179802-C-T			Uncertain significance (May 01, 2023)
5-138179811-C-T			Likely benign (Mar 01, 2024)
5-138179815-C-T			Likely benign (Jan 31, 2024)
5-138179819-T-C			Uncertain significance (Dec 07, 2023)
5-138179821-T-C			Likely benign (Jun 07, 2022)
5-138179822-A-G		not specified	Uncertain significance (Jan 04, 2022)
5-138179826-C-T			Uncertain significance (Aug 27, 2023)
5-138179857-G-T			Likely benign (Nov 20, 2022)
5-138179858-G-A			Likely benign (May 04, 2022)
5-138181405-C-G			Likely benign (May 09, 2022)
5-138181409-G-T			Likely benign (Oct 27, 2023)
5-138181424-T-C			Likely benign (Jun 27, 2022)
5-138181425-C-G			Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF20A	protein_coding	protein_coding	ENST00000394894	18	8997

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.53e-13	0.999	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	414	494	0.837	0.0000276	5812
Missense in Polyphen		155	183.45	0.84492		2051
Synonymous	0.121	181	183	0.989	0.00000876	1745
Loss of Function	3.10	29	53.4	0.543	0.00000303	562

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000561	0.000561
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000490	0.000489
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000265	0.000264
Middle Eastern	0.000490	0.000489
South Asian	0.000328	0.000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitotic kinesin required for chromosome passenger complex (CPC)-mediated cytokinesis. Following phosphorylation by PLK1, involved in recruitment of PLK1 to the central spindle. Interacts with guanosine triphosphate (GTP)-bound forms of RAB6A and RAB6B. May act as a motor required for the retrograde RAB6 regulated transport of Golgi membranes and associated vesicles along microtubules. Has a microtubule plus end-directed motility. {ECO:0000269|PubMed:12939256}.
• 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;Mitotic Telophase/Cytokinesis;M Phase;Cell Cycle;Cell Cycle, Mitotic;Aurora B signaling;PLK1 signaling events;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.892
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.53

Haploinsufficiency Scores

• pHI: 0.433
• hipred: Y
• hipred_score: 0.678
• ghis: 0.689

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.459

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kif20a
• 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); hematopoietic system phenotype; vision/eye phenotype

Zebrafish Information Network

• Gene name: kif20a
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: mitotic cytokinesis;microtubule bundle formation;microtubule-based movement;protein transport;vesicle-mediated transport;regulation of cytokinesis;midbody abscission
• Cellular component: nucleus;nucleoplasm;Golgi apparatus;spindle;kinesin complex;microtubule;midbody;cleavage furrow;intercellular bridge
• Molecular function: microtubule motor activity;transporter activity;protein binding;ATP binding;microtubule binding;ATPase activity;protein kinase binding