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NM_006415.4(SPTLC1):c.992C>T (p.Ser331Phe) AND Neuropathy, hereditary sensory and autonomic, type IA, severe

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 1, 2009
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:
RCV000005071.3

Allele description [Variation Report for NM_006415.4(SPTLC1):c.992C>T (p.Ser331Phe)]

NM_006415.4(SPTLC1):c.992C>T (p.Ser331Phe)

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>T (p.Ser331Phe)
HGVS:
  • NC_000009.12:g.92047261G>A
  • NG_007950.1:g.73148C>T
  • NM_001281303.2:c.992C>T
  • NM_001368272.1:c.626C>T
  • NM_001368273.1:c.527C>T
  • NM_006415.4:c.992C>TMANE SELECT
  • NP_001268232.1:p.Ser331Phe
  • NP_001355201.1:p.Ser209Phe
  • NP_001355202.1:p.Ser176Phe
  • NP_006406.1:p.Ser331Phe
  • LRG_272t1:c.992C>T
  • LRG_272:g.73148C>T
  • LRG_272p1:p.Ser331Phe
  • NC_000009.11:g.94809543G>A
  • O15269:p.Ser331Phe
Protein change:
S176F; SER331PHE
Links:
UniProtKB: O15269#VAR_066245; OMIM: 605712.0005; dbSNP: rs267607087
NCBI 1000 Genomes Browser:
rs267607087
Molecular consequence:
  • NM_001281303.2:c.992C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368272.1:c.626C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368273.1:c.527C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006415.4:c.992C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Neuropathy, hereditary sensory and autonomic, type IA, severe
Identifiers:
MedGen: C5231533

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000025247OMIM
no assertion criteria provided
Pathogenic
(Oct 1, 2009)
germlineliterature only

PubMed (3)
[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

Genes for hereditary sensory and autonomic neuropathies: a genotype-phenotype correlation.

Rotthier A, Baets J, De Vriendt E, Jacobs A, Auer-Grumbach M, Lévy N, Bonello-Palot N, Kilic SS, Weis J, Nascimento A, Swinkels M, Kruyt MC, Jordanova A, De Jonghe P, Timmerman V.

Brain. 2009 Oct;132(Pt 10):2699-711. doi: 10.1093/brain/awp198. Epub 2009 Aug 3.

PubMed [citation]
PMID:
19651702
PMCID:
PMC2759337

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
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000025247.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In a French Gypsy with hereditary sensory and autonomic neuropathy type I (HSAN1A; 162400), Rotthier et al. (2009) identified a de novo heterozygous 992C-T transition in the SPTLC1 gene, resulting in a ser331-to-phe (S331F) substitution in a conserved residue. The patient had an unusually severe phenotype, with congenital onset, insensitivity to pain with eschar and foot ulceration, pes cavus/equinovarus, vocal cord paralysis, and gastroesophageal reflux. The patient also had severe growth and mental retardation, microcephaly, hypotonia, amyotrophy, and respiratory insufficiency. Nerve conduction studies showed absent sensory and motor responses in the upper and lower limbs. The mutation was absent from 600 control chromosomes. The phenotype expanded the clinical spectrum of HSAN1.

Auer-Grumbach et al. (2013) reported that a patient with a severe form of HSAN1, originally described by Huehne et al. (2008) (patient ER-CIPA-20374), was found to be heterozygous for the S331F mutation in the SPTLC1 gene. The authors noted that another patient with a severe form of HSAN1 was heterozygous for a different mutation at ser311 in the SPTLC1 gene (S311Y; 605712.0007). Auer-Grumbach et al. (2013) confirmed increased 1-deoxySL formation in HEK293 cells expressing the S331F or the S331Y mutant. Canonical serine activity was reduced by 60% in both mutants.

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

Last Updated: May 6, 2023