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NM_002506.3(NGF):c.52G>T (p.Ala18Ser) AND Congenital sensory neuropathy with selective loss of small myelinated fibers

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 15, 2020
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:
RCV001205524.7

Allele description

NM_002506.3(NGF):c.52G>T (p.Ala18Ser)

Genes:
NGF-AS1:NGF antisense RNA 1 [Gene - HGNC]
NGF:nerve growth factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p13.2
Genomic location:
Preferred name:
NM_002506.3(NGF):c.52G>T (p.Ala18Ser)
HGVS:
  • NC_000001.11:g.115286744C>A
  • NG_007944.1:g.56493G>T
  • NM_002506.3:c.52G>TMANE SELECT
  • NP_002497.2:p.Ala18Ser
  • LRG_260t1:c.52G>T
  • LRG_260:g.56493G>T
  • NC_000001.10:g.115829365C>A
  • NM_002506.2:c.52G>T
Protein change:
A18S
Links:
dbSNP: rs1653523153
NCBI 1000 Genomes Browser:
rs1653523153
Molecular consequence:
  • NM_002506.3:c.52G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Congenital sensory neuropathy with selective loss of small myelinated fibers (HSAN5)
Synonyms:
INSENSITIVITY TO PAIN, CONGENITAL; HSAN Type V
Identifiers:
MONDO: MONDO:0012092; MedGen: C0020075; Orphanet: 64752; OMIM: 608654

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001376786Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Feb 15, 2020) 		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 Invitae, SCV001376786.5

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

Description

This variant has not been reported in the literature in individuals with NGF-related conditions. 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 disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with serine at codon 18 of the NGF protein (p.Ala18Ser). The alanine residue is highly conserved and there is a moderate physicochemical difference between alanine and serine.

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

Last Updated: Feb 28, 2024