KIF1C

kinesin family member 1C, the group of Kinesins

Basic information

Region (hg38): 17:4997950-5028401

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 (486 variants)
Inborn_genetic_diseases (160 variants)
not_provided (158 variants)
Hereditary_spastic_paraplegia (59 variants)
not_specified (37 variants)
KIF1C-related_disorder (16 variants)
Cerebellar_ataxia (1 variants)
Abnormal_central_motor_function (1 variants)
Spastic_ataxia (1 variants)
Microcephaly (1 variants)
Intellectual_disability (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. These statistics are base on transcript: NM_000006612.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	4 clinvar	154 clinvar	11 clinvar	170
missense	1 clinvar	6 clinvar	284 clinvar	37 clinvar	2 clinvar	330
nonsense	4 clinvar	2 clinvar	2 clinvar			8
start loss		1				1
frameshift	8 clinvar	4 clinvar	2 clinvar			14
splice donor/acceptor (+/-2bp)	1 clinvar	6 clinvar				7
Total	14	20	292	191	13

Highest pathogenic variant AF is 0.00000743513

Loading clinvar variants...

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