U.S. flag

An official website of the United States government

NM_006415.4(SPTLC1):c.992C>A (p.Ser331Tyr) AND Amyotrophic lateral sclerosis 27, juvenile

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 14, 2023
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003152600.1

Allele description [Variation Report for NM_006415.4(SPTLC1):c.992C>A (p.Ser331Tyr)]

NM_006415.4(SPTLC1):c.992C>A (p.Ser331Tyr)

Gene:
SPTLC1:serine palmitoyltransferase long chain base subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q22.31
Genomic location:
Preferred name:
NM_006415.4(SPTLC1):c.992C>A (p.Ser331Tyr)
HGVS:
  • NC_000009.12:g.92047261G>T
  • NG_007950.1:g.73148C>A
  • NM_001281303.2:c.992C>A
  • NM_001368272.1:c.626C>A
  • NM_001368273.1:c.527C>A
  • NM_006415.4:c.992C>AMANE SELECT
  • NP_001268232.1:p.Ser331Tyr
  • NP_001355201.1:p.Ser209Tyr
  • NP_001355202.1:p.Ser176Tyr
  • NP_006406.1:p.Ser331Tyr
  • LRG_272t1:c.992C>A
  • LRG_272:g.73148C>A
  • NC_000009.11:g.94809543G>T
  • NM_006415.2:c.992C>A
  • NM_006415.3:c.992C>A
Note:
NCBI staff developed the HGVS expression for this allele given that the only substitution that could generate S331Y is C>A. The paper by Auer-Grumbach et al., 2013 ((PubMed 23454272) described this as c.992G->T.
Protein change:
S176Y; SER331TYR
Links:
OMIM: 605712.0007; dbSNP: rs267607087
NCBI 1000 Genomes Browser:
rs267607087
Molecular consequence:
  • NM_001281303.2:c.992C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368272.1:c.626C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368273.1:c.527C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006415.4:c.992C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Amyotrophic lateral sclerosis 27, juvenile (ALS27)
Identifiers:
MONDO: MONDO:0859529; MedGen: C5830359; OMIM: 620285

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV003841238OMIM
no assertion criteria provided
Pathogenic
(Mar 14, 2023)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutations at Ser331 in the HSN type I gene SPTLC1 are associated with a distinct syndromic phenotype.

Auer-Grumbach M, Bode H, Pieber TR, Schabhüttl M, Fischer D, Seidl R, Graf E, Wieland T, Schuh R, Vacariu G, Grill F, Timmerman V, Strom TM, Hornemann T.

Eur J Med Genet. 2013 May;56(5):266-9. doi: 10.1016/j.ejmg.2013.02.002. Epub 2013 Feb 27.

PubMed [citation]
PMID:
23454272
PMCID:
PMC3682180

Association of Variants in the SPTLC1 Gene With Juvenile Amyotrophic Lateral Sclerosis.

Johnson JO, Chia R, Miller DE, Li R, Kumaran R, Abramzon Y, Alahmady N, Renton AE, Topp SD, Gibbs JR, Cookson MR, Sabir MS, Dalgard CL, Troakes C, Jones AR, Shatunov A, Iacoangeli A, Al Khleifat A, Ticozzi N, Silani V, Gellera C, Blair IP, et al.

JAMA Neurol. 2021 Oct 1;78(10):1236-1248. doi: 10.1001/jamaneurol.2021.2598.

PubMed [citation]
PMID:
34459874
PMCID:
PMC8406220

Details of each submission

From OMIM, SCV003841238.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Hereditary Sensory and Autonomic Neuropathy, Type IA

In a girl, born of nonconsanguineous parents, with hereditary sensory and autonomic neuropathy type I (HSAN1A; 162400), Auer-Grumbach et al. (2013) identified a de novo heterozygous c.922G-T transversion in the SPTLC1 gene, resulting in a ser311-to-tyr (S311Y) substitution. The mutation segregated with the disorder in the family and was not found in 1,969 individuals in an in-house database. The girl had a severe form of the disorder, with onset at age 4 years of unsteady gait, hand tremor, progressive sensory disturbances, and a pes cavus foot deformity necessitating triple arthrodesis at age 5. Disease progression was rapid and led to severe scoliosis, respiratory problems, and wheelchair dependence at age 14. She had prominent growth retardation but normal intellectual development. The level of 1-deoxySL was significantly elevated in the patient's plasma. Auer-Grumbach et al. (2013) noted that a different mutation at ser331 in the SPTLC1 gene (S331F; 605712.0005) resulted in a severe form of the disorder in 2 patients with HSAN1. They confirmed increased 1-deoxySL formation in HEK293 cells expressing the S331Y or the S331F mutant. Canonical serine activity was reduced by 60% in both mutants.

Juvenile Amyotrophic Lateral Sclerosis 27

In a patient (patient 3) with juvenile amyotrophic lateral sclerosis-27 (ALS27; 620285), Johnson et al. (2021) identified heterozygosity for the S331Y mutation. The mutation was identified by whole-exome sequencing and shown to be de novo. The patient had prominent motor symptoms and modest sensory autonomic symptoms.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 25, 2025