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SPTLC1

Synonyms
HSAN1, HSN1, LBC1, LCB1, SPT1, SPTI
External resources
Summary
This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13.

Variant counts

The variants found in rare patients tested by 3billion are classified and counted according to ACMG guidelines. The variants with over 5% variant frequency in population genome databases ( gnomAD, dbSNP, etc) are excluded.

Pathogenic
6
Likely pathogenic
1
VUS
1,146
Likely benign
724
Benign
12,923

Patient phenotypes

Proportions of phenotypes among 7 patients carrying pathogenic or likely pathogenic variants on SPTLC1 gene are displayed below.

Phenotype class
Patients in 3billion (%)
Abnormality of the musculoskeletal system
42.9%
Abnormality of head or neck
28.6%
Abnormality of the nervous system
28.6%
Abnormality of the ear
14.3%
Abnormality of the eye
14.3%
Abnormality of the immune system
14.3%
Abnormality of the integument
14.3%
Constitutional symptom
14.3%
Growth abnormality
14.3%
Abnormal cellular phenotype
0%
Abnormality of blood and blood-forming tissues
0%
Abnormality of limbs
0%
Abnormality of metabolism homeostasis
0%
Abnormality of prenatal development or birth
0%
Abnormality of the breast
0%
Abnormality of the cardiovascular system
0%
Abnormality of the digestive system
0%
Abnormality of the endocrine system
0%
Abnormality of the genitourinary system
0%
Abnormality of the respiratory system
0%
Abnormality of the thoracic cavity
0%
Abnormality of the voice
0%
Neoplasm
0%

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