KIF3C

kinesin family member 3C, the group of Kinesins

Basic information

Region (hg38): 2:25926598-25982749

Links

ENSG00000084731 ∙ NCBI:3797 ∙ OMIM:602845 ∙ HGNC:6321 ∙ Uniprot:O14782 ∙ 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 KIF3C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF3C 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						0
missense			28	1		29
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in KIF3C

This is a list of pathogenic ClinVar variants found in the KIF3C region.

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

Position	Type	Phenotype	Significance	ClinVar
2-25929006-C-T		not specified	Likely benign (Jan 26, 2022)
2-25929007-G-A		not specified	Uncertain significance (Dec 09, 2023)
2-25929024-A-G		not specified	Uncertain significance (Dec 16, 2023)
2-25929027-G-C		not specified	Uncertain significance (Jan 24, 2023)
2-25929320-C-T		not specified	Uncertain significance (Apr 17, 2024)
2-25929355-G-C		not specified	Uncertain significance (Oct 14, 2023)
2-25929464-A-G		not specified	Uncertain significance (Jun 28, 2023)
2-25930048-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-25951822-T-C		not specified	Uncertain significance (May 17, 2023)
2-25951874-C-G		not specified	Uncertain significance (May 31, 2023)
2-25954268-T-G		not specified	Uncertain significance (Jan 25, 2023)
2-25955609-T-C		not specified	Uncertain significance (Dec 14, 2023)
2-25955624-G-A		not specified	Uncertain significance (Jun 10, 2024)
2-25955641-T-C		not specified	Uncertain significance (Feb 06, 2024)
2-25955645-T-A		not specified	Uncertain significance (Dec 13, 2022)
2-25955656-C-T		not specified	Uncertain significance (Mar 14, 2023)
2-25956404-A-G		not specified	Uncertain significance (Sep 01, 2021)
2-25980413-C-T		not specified	Uncertain significance (Feb 27, 2024)
2-25980432-T-G		not specified	Uncertain significance (Jun 27, 2022)
2-25980503-T-G		not specified	Uncertain significance (Mar 31, 2024)
2-25980634-C-G		not specified	Uncertain significance (Sep 20, 2023)
2-25980704-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-25980767-T-C		not specified	Uncertain significance (Sep 07, 2022)
2-25980927-C-G		not specified	Uncertain significance (Sep 22, 2023)
2-25981103-C-T		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF3C	protein_coding	protein_coding	ENST00000264712	8	56148

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.992	0.00847	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	358	508	0.705	0.0000326	5213
Missense in Polyphen		97	184.93	0.52451		1956
Synonymous	1.31	186	210	0.885	0.0000135	1598
Loss of Function	4.58	4	31.9	0.125	0.00000178	348

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-based anterograde translocator for membranous organelles. {ECO:0000250}.
• 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;Intraflagellar transport;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.254
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.67

Haploinsufficiency Scores

• pHI: 0.274
• hipred: Y
• hipred_score: 0.662
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kif3c
• 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); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: kif3cb
• Affected structure: photoreceptor outer segment layer
• Phenotype tag: abnormal
• Phenotype quality: decreased variability of size

Gene ontology

• Biological process: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based movement;antigen processing and presentation of exogenous peptide antigen via MHC class II;intraciliary transport involved in cilium assembly;organelle transport along microtubule
• Cellular component: cytosol;kinesin complex;microtubule;cilium;ciliary tip
• Molecular function: motor activity;microtubule motor activity;ATP binding;microtubule binding;ATPase activity