SPG11

Chr 15

SPG11 vesicle trafficking associated, spatacsin

Also known as: ALS5, CMT2X, KIAA1840

The protein encoded by this gene is a potential transmembrane protein that is phosphorylated upon DNA damage. Defects in this gene are a cause of spastic paraplegia type 11 (SPG11). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtSpastic paraplegia 11, autosomal recessive
UniProtAmyotrophic lateral sclerosis 5, juvenile
UniProtCharcot-Marie-Tooth disease, axonal, type 2X

Clinical highlights

Gene-disease validity (ClinGen)
hereditary spastic paraplegia 11 · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
3
Active trials
46
Pubs (1 yr)
P/LP submissions
P/LP missense
0.81
LOEUF
LOF
Mechanism· G2P
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
0.81LOEUF
pLI 0.000
Z-score 3.30
OE 0.67 (0.560.81)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
-1.39Z-score
OE missense 1.11 (1.061.16)
1360 obs / 1223.0 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?
LoF OE?0.67 (0.560.81)
00.351.4
Missense OE?1.11 (1.061.16)
00.61.4
Synonymous OE?1.13
01.21.6
LoF obs/exp: 81 / 120.0Missense obs/exp: 1360 / 1223.0Syn Z: -2.17

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SPG11 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.