KIF1C

kinesin family member 1C, the group of Kinesins

Basic information

Region (hg38): 17:4997949-5028401

Previous symbols: [ "SAX2" ]

Links

ENSG00000129250 ∙ NCBI:10749 ∙ OMIM:603060 ∙ HGNC:6317 ∙ Uniprot:O43896 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spastic ataxia 2 (Moderate), mode of inheritance: AR
• spastic ataxia 2 (Strong), mode of inheritance: AR
• spastic ataxia 2 (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic ataxia 2, autosomal recessive	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	Neurologic	24319291; 24482476

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIF1C gene.

• Spastic ataxia 2 (416 variants)
• not provided (151 variants)
• Hereditary spastic paraplegia (63 variants)
• Inborn genetic diseases (62 variants)
• not specified (38 variants)
• KIF1C-related condition (2 variants)
• Abnormal central motor function (1 variants)
• Intellectual disability (1 variants)
• Cerebellar ataxia (1 variants)
• Microcephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF1C 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			4	108	15	127
missense	1	5	199	12	3	220
nonsense	3	2	1			6
start loss		1				1
frameshift	6	2	2			10
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	2				3
splice region		1	18	21	3	43
non coding			2	76	37	115
Total	11	12	209	196	55

Highest pathogenic variant AF is 0.00000657

Variants in KIF1C

This is a list of pathogenic ClinVar variants found in the KIF1C region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4998136-C-G		not specified	Likely benign (Aug 07, 2017)
17-4998169-G-C		not specified	Benign (Nov 24, 2017)
17-4998172-G-A		not specified	Likely benign (Feb 02, 2018)
17-4999663-G-A			Benign (Mar 28, 2022)
17-4999857-C-T		not specified	Likely benign (Apr 05, 2017)
17-4999978-G-A		not specified	Likely benign (Feb 06, 2018)
17-5000100-T-C			Benign (Sep 18, 2018)
17-5000249-G-T			Likely pathogenic (Oct 23, 2020)
17-5000256-G-T		Spastic ataxia 2 • Inborn genetic diseases	Uncertain significance (Jan 17, 2024)
17-5000260-C-T		Spastic ataxia 2	Likely benign (Aug 10, 2022)
17-5000261-G-A		Spastic ataxia 2	Benign (Mar 02, 2023)
17-5000264-G-A		Hereditary spastic paraplegia • Spastic ataxia 2	Conflicting classifications of pathogenicity (Aug 04, 2023)
17-5000283-C-T		Spastic ataxia 2	Uncertain significance (Nov 27, 2017)
17-5000287-C-T		Spastic ataxia 2	Likely pathogenic (Feb 23, 2023)
17-5000294-C-T		Spastic ataxia 2	Likely benign (Mar 20, 2023)
17-5000297-C-T		Spastic ataxia 2	Likely benign (Oct 05, 2020)
17-5000299-G-A		Spastic ataxia 2	Uncertain significance (Mar 31, 2022)
17-5000322-T-C		Spastic ataxia 2	Likely benign (Jun 02, 2022)
17-5000366-C-T		Spastic ataxia 2	Likely benign (Aug 10, 2023)
17-5000367-G-A		Spastic ataxia 2	Likely benign (May 20, 2022)
17-5000694-G-A			Likely benign (May 28, 2021)
17-5000756-C-T		Spastic ataxia 2	Likely benign (Nov 24, 2022)
17-5000765-C-T		Spastic ataxia 2	Likely benign (Jan 28, 2022)
17-5000767-C-T		Spastic ataxia 2	Likely benign (Jan 05, 2023)
17-5000774-A-G		Spastic ataxia 2	Uncertain significance (Feb 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF1C	protein_coding	protein_coding	ENST00000320785	21	30454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.718	0.282	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	585	688	0.850	0.0000449	7021
Missense in Polyphen		64	97.634	0.65551		998
Synonymous	-1.29	295	268	1.10	0.0000165	2266
Loss of Function	5.52	12	57.0	0.211	0.00000323	605

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000197	0.000185
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Motor required for the retrograde transport of Golgi vesicles to the endoplasmic reticulum. Has a microtubule plus end- directed motility. {ECO:0000269|PubMed:9685376}.
• Disease: DISEASE: Spastic ataxia 2, autosomal recessive (SPAX2) [MIM:611302]: A neurologic disorder characterized by cerebellar ataxia, dysarthria, and variable spasticity of the lower limbs. Cognition is not affected. {ECO:0000269|PubMed:24319291, ECO:0000269|PubMed:24482476}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• 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: 0.163

Intolerance Scores

• loftool: 0.237
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.14

Haploinsufficiency Scores

• pHI: 0.761
• hipred: Y
• hipred_score: 0.637
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.719

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kif1c
• Phenotype: endocrine/exocrine gland phenotype; normal phenotype; reproductive system phenotype; immune system phenotype

Gene ontology

• Biological process: retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;microtubule-based movement;vesicle-mediated transport;cytoskeleton-dependent intracellular transport;anterograde neuronal dense core vesicle transport;retrograde neuronal dense core vesicle transport
• Cellular component: endoplasmic reticulum;Golgi apparatus;kinesin complex;microtubule;axon;dendrite;neuron projection;axon cytoplasm
• Molecular function: RNA binding;motor activity;microtubule motor activity;protein binding;ATP binding;microtubule binding;ATP-dependent microtubule motor activity, plus-end-directed;ATPase activity