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

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

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

Recent activity

Clear Turn Off Turn On

Mus musculus protein phosphatase 1, regulatory (inhibitor) subunit 14D, mRNA (cD...
Mus musculus protein phosphatase 1, regulatory (inhibitor) subunit 14D, mRNA (cDNA clone MGC:37622 IMAGE:4989982), complete cds
gi|19354014|gb|BC024547.1|

Nucleotide
Mus musculus 12 days embryo eyeball cDNA, RIKEN full-length enriched library, cl...
Mus musculus 12 days embryo eyeball cDNA, RIKEN full-length enriched library, clone:D230009J11 product:EGF-like repeats and discordin I-like domains 3, full insert sequence
gi|26351006|dbj|AK084215.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001376786	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 15, 2020)	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

SCV001376786

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 15, 2020)

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, SCV001376786.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	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

ClinVar

Relating variation to medicine