NM_006415.4(SPTLC1):c.509C>T (p.Thr170Ile) AND Hereditary sensory and autonomic neuropathy type 1

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 9, 2023
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:: RCV003613250.1

Allele description

NM_006415.4(SPTLC1):c.509C>T (p.Thr170Ile)

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.509C>T (p.Thr170Ile)

HGVS:

NC_000009.12:g.92068017G>A
NG_007950.1:g.52392C>T
NM_001281303.2:c.509C>T
NM_001368272.1:c.143C>T
NM_001368273.1:c.44C>T
NM_006415.4:c.509C>TMANE SELECT
NP_001268232.1:p.Thr170Ile
NP_001355201.1:p.Thr48Ile
NP_001355202.1:p.Thr15Ile
NP_006406.1:p.Thr170Ile
NP_006406.1:p.Thr170Ile
LRG_272t1:c.509C>T
LRG_272:g.52392C>T
LRG_272p1:p.Thr170Ile
NC_000009.11:g.94830299G>A
NM_006415.2:c.509C>T

Protein change:

T15I

Molecular consequence:

NM_001281303.2:c.509C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368272.1:c.143C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001368273.1:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006415.4:c.509C>T - 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
SCV004448615	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 9, 2023)	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

SCV004448615

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 9, 2023)

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 Invitae, SCV004448615.1

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

Description

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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SPTLC1 protein function. This variant has not been reported in the literature in individuals affected with SPTLC1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 170 of the SPTLC1 protein (p.Thr170Ile).

#	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: Feb 28, 2024

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