KIF25

kinesin family member 25, the group of Kinesins

Basic information

Region (hg38): 6:167996241-168045091

Previous symbols: [ "KNSL3" ]

Links

ENSG00000125337 ∙ ∙ OMIM:603815 ∙ HGNC:6390 ∙ Uniprot:Q9UIL4 ∙ 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 KIF25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF25 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		3
missense			31		2	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	3	2

Variants in KIF25

This is a list of pathogenic ClinVar variants found in the KIF25 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-168030793-C-T		not specified	Uncertain significance (Apr 25, 2022)
6-168030801-G-A			Benign (Apr 19, 2018)
6-168030818-G-A			Likely benign (Feb 01, 2023)
6-168030820-G-A		not specified	Uncertain significance (Feb 15, 2023)
6-168030831-A-T		not specified	Uncertain significance (Aug 02, 2021)
6-168033900-G-A		not specified	Uncertain significance (Apr 06, 2023)
6-168033923-G-A		not specified	Uncertain significance (Aug 10, 2021)
6-168033937-A-G		not specified	Uncertain significance (Dec 20, 2023)
6-168033953-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-168033974-C-T		not specified	Uncertain significance (Nov 19, 2022)
6-168033981-C-A		not specified	Likely benign (Mar 26, 2024)
6-168034001-T-G		not specified	Uncertain significance (Dec 12, 2023)
6-168034004-T-C		not specified	Uncertain significance (May 01, 2022)
6-168034009-A-G		not specified	Uncertain significance (Dec 19, 2022)
6-168038572-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-168038609-T-C		not specified	Uncertain significance (Oct 06, 2022)
6-168038646-C-G		not specified	Uncertain significance (Mar 20, 2024)
6-168038653-G-T		not specified	Uncertain significance (May 25, 2022)
6-168038678-A-T		not specified	Uncertain significance (May 02, 2024)
6-168038683-G-C		not specified	Uncertain significance (Jul 11, 2023)
6-168040072-G-C		not specified	Uncertain significance (Jan 06, 2023)
6-168040078-G-A		not specified	Uncertain significance (Apr 20, 2023)
6-168040090-A-T		not specified	Uncertain significance (Mar 04, 2024)
6-168040098-C-T		not specified	Likely benign (Feb 12, 2024)
6-168040135-A-G		not specified	Uncertain significance (May 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF25	protein_coding	protein_coding	ENST00000443060	8	48849

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.64e-7	0.550	125568	3	177	125748	0.000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.573	216	241	0.896	0.0000151	2418
Missense in Polyphen		78	82.416	0.94641		913
Synonymous	0.107	104	105	0.987	0.00000732	823
Loss of Function	0.876	11	14.6	0.753	6.87e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00187	0.00187
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.00426	0.00412
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Minus-end microtubule-dependent motor protein (By similarity). Acts as a negative regulator of centrosome separation required to prevent premature centrosome separation during interphase (PubMed:28263957). Required to maintain a centered nucleus to ensure that the spindle is stably oriented at the onset of mitosis (PubMed:28263957). May also act as a negative regulator of amino acid starvation-induced autophagy (PubMed:22354037). {ECO:0000250|UniProtKB:Q4R918, ECO:0000269|PubMed:22354037, ECO:0000269|PubMed:28263957}.
• 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: 0.0878

Intolerance Scores

• loftool: 0.843
• rvis_EVS: 1.94
• rvis_percentile_EVS: 97.51

Haploinsufficiency Scores

• pHI: 0.0486
• hipred: N
• hipred_score: 0.219

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00224

Gene Damage Prediction

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

Gene ontology

• Biological process: mitotic sister chromatid segregation;organelle organization;microtubule-based movement;negative regulation of autophagy;negative regulation of mitotic centrosome separation;protein homotetramerization;establishment of spindle orientation;nucleus localization
• Cellular component: cytoplasm;centrosome;kinesin complex;microtubule
• Molecular function: microtubule motor activity;ATP binding;microtubule binding;ATP-dependent microtubule motor activity, minus-end-directed;ATPase activity