KIF1C

Chr 17AR

kinesin family member 1C

Also known as: LTXS1, SATX2, SAX2, SPAX2, SPG58

NCBI Gene: 10749 ENSG00000129250 UniProt: O43896 OMIM: 603060

KIF1C encodes a kinesin motor protein required for retrograde transport of Golgi vesicles to the endoplasmic reticulum and has microtubule plus end-directed motility. Mutations cause spastic ataxia 2, an autosomal recessive disorder affecting the central nervous system with both spasticity and ataxia features. The gene shows significant constraint against loss-of-function variants (LOEUF 0.341), suggesting intolerance to protein disruption.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

The protein encoded by this gene is a member of the kinesin-like protein family. The family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. Mutations in this gene are a cause of spastic ataxia 2, autosomal recessive. [provided by RefSeq, May 2014]

OMIM ResearchGenerating clinical summary…

ARLOEUF 0.341 OMIM phenotype

Clinical Summary— KIF1C

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.72) — some intolerance to loss-of-function variants.

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ClinVar Variants

41 unique Pathogenic / Likely Pathogenic· 343 VUS of 810 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.34LOEUF

pLI 0.718

Z-score 5.52

OE 0.21 (0.13–0.34)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

1.40Z-score

OE missense 0.85 (0.79–0.91)

585 obs / 688.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.21 (0.13–0.34)

0≤0.351.4

Missense OE?0.85 (0.79–0.91)

0≤0.61.4

Synonymous OE?1.10

0≤1.21.6

LoF obs/exp: 12 / 57.0Missense obs/exp: 585 / 688.5Syn Z: -1.29

ClinVar Variant Classifications

810 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic16

Likely Pathogenic25

VUS343

Likely Benign303

Benign57

Conflicting39

Pathogenic

Likely Pathogenic

343

VUS

303

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	13	1	2	0	16
Likely Pathogenic	17	7	0	1	25
VUS	5	312	22	4	343
Likely Benign	0	16	130	157	303
Benign	0	3	40	14	57
Conflicting	—				39
Total	35	339	194	176	783

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

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24 pathogenic / likely-pathogenic (of 37) ClinVar copy-number / structural variants overlap KIF1C — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →