NM_006415.4(SPTLC1):c.1216G>A (p.Glu406Lys) AND Hereditary sensory and autonomic neuropathy type 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 4, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001315181.7

Allele description [Variation Report for NM_006415.4(SPTLC1):c.1216G>A (p.Glu406Lys)]

NM_006415.4(SPTLC1):c.1216G>A (p.Glu406Lys)

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.1216G>A (p.Glu406Lys)

HGVS:

NC_000009.12:g.92038286C>T
NG_007950.1:g.82123G>A
NM_001281303.2:c.1216G>A
NM_001368272.1:c.850G>A
NM_001368273.1:c.751G>A
NM_006415.4:c.1216G>AMANE SELECT
NP_001268232.1:p.Glu406Lys
NP_001355201.1:p.Glu284Lys
NP_001355202.1:p.Glu251Lys
NP_006406.1:p.Glu406Lys
LRG_272:g.82123G>A
NC_000009.11:g.94800568C>T

Protein change:

E251K

Links:

dbSNP: rs750753414

NCBI 1000 Genomes Browser:

rs750753414

Molecular consequence:

NM_001281303.2:c.1216G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368272.1:c.850G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001368273.1:c.751G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006415.4:c.1216G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary sensory and autonomic neuropathy type 1 (HSAN1)
Synonyms:: HSAN 1; Neuropathy hereditary sensory radicular, autosomal dominant; Hereditary sensory neuropathy type 1; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0018213; MedGen: C0020071; Orphanet: 36386

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001505742	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 4, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001505742

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 4, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001505742.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 406 of the SPTLC1 protein (p.Glu406Lys). This variant is present in population databases (rs750753414, gnomAD 0.01%). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1016208). This variant has not been reported in the literature in individuals affected with SPTLC1-related conditions.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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