NM_004863.4(SPTLC2):c.1440C>T (p.Gly480=) AND Neuropathy, hereditary sensory and autonomic, type 1C

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 18, 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:
RCV003527342.2

Allele description [Variation Report for NM_004863.4(SPTLC2):c.1440C>T (p.Gly480=)]

NM_004863.4(SPTLC2):c.1440C>T (p.Gly480=)

Gene:
SPTLC2:serine palmitoyltransferase long chain base subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q24.3
Genomic location:
Preferred name:
NM_004863.4(SPTLC2):c.1440C>T (p.Gly480=)
HGVS:
  • NC_000014.9:g.77518167G>A
  • NG_028282.1:g.103601C>T
  • NM_004863.4:c.1440C>TMANE SELECT
  • NP_004854.1:p.Gly480=
  • NP_004854.1:p.Gly480=
  • LRG_371t1:c.1440C>T
  • LRG_371:g.103601C>T
  • LRG_371p1:p.Gly480=
  • NC_000014.8:g.77984510G>A
  • NM_004863.3:c.1440C>T
Molecular consequence:
  • NM_004863.4:c.1440C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Neuropathy, hereditary sensory and autonomic, type 1C
Synonyms:
HSAN IC; HSN IC; Hereditary sensory and autonomic neuropathy type IC
Identifiers:
MONDO: MONDO:0013337; MedGen: C3150896; Orphanet: 36386; OMIM: 613640

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004369853Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 18, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV004369853.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change affects codon 480 of the SPTLC2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SPTLC2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs780807321, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with SPTLC2-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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.

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

Last Updated: Sep 29, 2024