KIFC3

kinesin family member C3, the group of Kinesins|MicroRNA protein coding host genes

Basic information

Region (hg38): 16:57758217-57863053

Links

ENSG00000140859 ∙ NCBI:3801 ∙ OMIM:604535 ∙ HGNC:6326 ∙ Uniprot:Q9BVG8 ∙ 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 KIFC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIFC3 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			51			51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	54	0	1

Variants in KIFC3

This is a list of pathogenic ClinVar variants found in the KIFC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-57759748-C-T		not specified	Uncertain significance (Aug 12, 2021)
16-57759754-G-T		not specified	Uncertain significance (May 04, 2022)
16-57759764-G-A		not specified	Uncertain significance (Apr 13, 2022)
16-57759817-G-A		not specified	Uncertain significance (Jan 27, 2022)
16-57760325-C-T		not specified	Uncertain significance (Jun 05, 2023)
16-57760832-G-C		not specified	Uncertain significance (May 25, 2022)
16-57760874-T-C		not specified	Uncertain significance (Mar 08, 2024)
16-57761044-G-A		not specified	Uncertain significance (Feb 22, 2023)
16-57761050-C-T		not specified	Uncertain significance (May 09, 2023)
16-57761083-G-A		not specified	Uncertain significance (Oct 18, 2021)
16-57761138-C-T		not specified	Uncertain significance (Jul 11, 2023)
16-57761448-C-G		not specified	Uncertain significance (Oct 05, 2021)
16-57762174-C-T		not specified	Uncertain significance (Jul 25, 2023)
16-57764166-C-T		not specified	Uncertain significance (Jan 29, 2024)
16-57764182-C-T			Benign (Apr 16, 2018)
16-57764183-G-T		not specified	Uncertain significance (Oct 12, 2021)
16-57765469-G-A		not specified	Uncertain significance (May 03, 2023)
16-57765550-T-G		not specified	Uncertain significance (Nov 18, 2023)
16-57765551-C-T		not specified	Uncertain significance (Jul 25, 2023)
16-57765571-T-C		not specified	Uncertain significance (Jun 21, 2022)
16-57765599-C-T		not specified	Uncertain significance (May 16, 2023)
16-57766907-T-C		not specified	Uncertain significance (Feb 26, 2024)
16-57766916-G-T		not specified	Uncertain significance (Jan 03, 2024)
16-57766927-C-G		not specified	Uncertain significance (Oct 12, 2021)
16-57766957-C-T		not specified	Uncertain significance (Jun 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIFC3	protein_coding	protein_coding	ENST00000379655	18	104829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00565	0.994	125672	0	69	125741	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	399	528	0.756	0.0000368	5293
Missense in Polyphen		109	173.46	0.62838		1696
Synonymous	0.883	210	227	0.925	0.0000157	1725
Loss of Function	4.42	13	45.0	0.289	0.00000269	455

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000360	0.000358
Ashkenazi Jewish	0.00283	0.00278
East Asian	0.0000571	0.0000544
Finnish	0.0000944	0.0000924
European (Non-Finnish)	0.000197	0.000193
Middle Eastern	0.0000571	0.0000544
South Asian	0.0000981	0.0000980
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Minus-end microtubule-dependent motor protein. Involved in apically targeted transport (By similarity). Required for zonula adherens maintenance. {ECO:0000250, ECO:0000269|PubMed:19041755}.
• Pathway: Ectoderm Differentiation;Metabolism of proteins;Chaperonin-mediated protein folding;Association of TriC/CCT with target proteins during biosynthesis;Protein folding;Stabilization and expansion of the E-cadherin adherens junction (Consensus)

Recessive Scores

• pRec: 0.0988

Intolerance Scores

• loftool: 0.577
• rvis_EVS: -1.82
• rvis_percentile_EVS: 2.16

Haploinsufficiency Scores

• pHI: 0.257
• hipred: Y
• hipred_score: 0.756
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.535

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kifc3

Gene ontology

• Biological process: microtubule-based movement;Golgi organization;visual perception;zonula adherens maintenance;epithelial cell-cell adhesion
• Cellular component: Golgi apparatus;centrosome;kinesin complex;microtubule;zonula adherens;cytoplasmic vesicle membrane;extracellular exosome
• Molecular function: microtubule motor activity;protein binding;ATP binding;microtubule binding;ATP-dependent microtubule motor activity, minus-end-directed;ATPase activity