HSN-1A

SPTLC1 | 2001

What Is HSN-1A?

HSN-1A is a type of CMT caused by autosomal dominant mutations in the SPTLC1 gene. This gene provides instructions for making part of an enzyme involved in the production of sphingolipids, a class of fats essential to nerve cell membranes. Mutations in the SPTLC1 gene disrupt this function, leading to impaired nerve signal transmission.

HSN-1A is autosomal dominant, meaning that just one of the gene’s two copies needs a mutation to cause this subtype.

Clinical Features

The age of symptom onset in HSN-1A is variable, ranging from childhood to adulthood. Symptoms typically begin in the lower extremities and progress over time to involve the upper limbs. Nerve conduction studies usually show somewhat slowed conduction velocities and reduced amplitudes, consistent with an axonal form of CMT.

HSN-1A symptoms may include:

  • Weakness in the feet and lower legs
  • Muscle atrophy
  • Foot drop
  • Reduced or absent reflexes
  • Reduced sensation
  • A steppage-style walking pattern
  • Foot deformities, including high arches, and hammertoes (clawed toes)
  • Progressive involvement of the hands and forearms
  • Difficulty with fine motor skills and manual dexterity
  • Additional symptoms not listed here

Disease Course

HSN-1A shows wide variability in severity and progression. Some individuals are mildly affected, while others develop a more severe disease. Disease progression is generally slow, and life expectancy is not reduced.

Clinical Basics

Subtype
HSN-1A

Classification
HSN

Neuropathy Type
Axonal

Inheritance Pattern
autosomal dominant

Genetic Context

HGNC-Approved Gene Symbol
SPTLC1

Gene Full Name
serine palmitoyltransferase long chain base subunit 1

Chromosome
9q22.31

Zygosity of Responsible Variant
Heterozygous

Variant Mechanism

Toxic Gain of Function (GoF)

Details

Mechanistic basis:
Neomorphic

Confidence:
High

Prediction:
Two recurrent SPTLC1 alleles anchor the prediction of a neomorphic gain of function in HSN-1A: C133W and V144D replace residues lining the substrate channel at the interface of the SPTLC1/SPTLC2 heterodimer, and the remodeled pocket admits alanine and glycine alongside serine, yielding neurotoxic 1-deoxysphingolipids. Sptlc1 knockout does not reproduce the sensory phenotype, and added wild-type enzyme fails to neutralize the atypical lipids, which the literature reads as an acquired activity rather than lost or disrupted function.

Rationale:
Neither test that would expose a loss comes back positive: removing Sptlc1 does not recreate the disease, and restoring normal enzyme leaves the 1-deoxysphingolipid burden in place. Both results point away from haploinsufficiency and away from interference with the partner subunit, and toward a mutant enzyme that manufactures something new by itself.

ClinVar Pathogenic Variants

View SPTLC1 ClinVar Variants

HSN-1A OMIM Entry

HSN-1A OMIM

SPTLC1 OMIM Entry

SPTLC1 OMIM

More Info

HSN-1A Research Opportunity

CMT Natural History Study

Original Discovery Publication

Publication Title

Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I

Authors

Dawkins, J. L., Hulme, D. J., Brahmbhatt, S. B., Auer-Grumbach, M., & Nicholson, G. A.

Publication Date
March 27, 2001

Updated: July 18, 2026 | By: K. Raymond

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