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NM_002529.4(NTRK1):c.53G>A (p.Gly18Glu) AND Hereditary insensitivity to pain with anhidrosis

Germline classification:
Benign/Likely benign (5 submissions)
Last evaluated:
Jan 31, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001081416.24

Allele description [Variation Report for NM_002529.4(NTRK1):c.53G>A (p.Gly18Glu)]

NM_002529.4(NTRK1):c.53G>A (p.Gly18Glu)

Gene:
NTRK1:neurotrophic receptor tyrosine kinase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q23.1
Genomic location:
Preferred name:
NM_002529.4(NTRK1):c.53G>A (p.Gly18Glu)
HGVS:
  • NC_000001.11:g.156860987G>A
  • NG_007493.1:g.50238G>A
  • NM_001007792.1:c.123-3367G>A
  • NM_001012331.2:c.53G>A
  • NM_002529.4:c.53G>AMANE SELECT
  • NP_001012331.1:p.Gly18Glu
  • NP_001012331.1:p.Gly18Glu
  • NP_002520.2:p.Gly18Glu
  • NP_002520.2:p.Gly18Glu
  • LRG_261t1:c.123-3367G>A
  • LRG_261t2:c.53G>A
  • LRG_261t3:c.53G>A
  • LRG_261:g.50238G>A
  • LRG_261p2:p.Gly18Glu
  • LRG_261p3:p.Gly18Glu
  • NC_000001.10:g.156830779G>A
  • NM_001012331.1:c.53G>A
  • NM_002529.3:c.53G>A
  • P04629:p.Gly18Glu
Protein change:
G18E
Links:
UniProtKB: P04629#VAR_049714; dbSNP: rs1007211
NCBI 1000 Genomes Browser:
rs1007211
Molecular consequence:
  • NM_001007792.1:c.123-3367G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001012331.2:c.53G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002529.4:c.53G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary insensitivity to pain with anhidrosis (CIPA)
Synonyms:
INSENSITIVITY TO PAIN, CONGENITAL, WITH ANHIDROSIS; FAMILIAL DYSAUTONOMIA, TYPE II; NEUROPATHY, CONGENITAL SENSORY, WITH ANHIDROSIS; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009746; MedGen: C0020074; Orphanet: 642; OMIM: 256800

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000626973Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 31, 2024)
germlineclinical testing

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

SCV000885864ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Benign
(Nov 17, 2023)
germlineclinical testing

Citation Link,

SCV001256073Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Benign
(Apr 27, 2017)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Citation Link,

SCV001653482Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(May 18, 2021)
germlineclinical testing

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

SCV004016478KCCC/NGS Laboratory, Kuwait Cancer Control Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benign
(Jul 7, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
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

Novel frameshift and splice site mutations in the neurotrophic tyrosine kinase receptor type 1 gene (NTRK1) associated with hereditary sensory neuropathy type IV.

Verpoorten N, Claeys KG, Deprez L, Jacobs A, Van Gerwen V, Lagae L, Arts WF, De Meirleir L, Keymolen K, Ceuterick-de Groote C, De Jonghe P, Timmerman V, Nelis E.

Neuromuscul Disord. 2006 Jan;16(1):19-25. Epub 2005 Dec 20.

PubMed [citation]
PMID:
16373086
See all PubMed Citations (9)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000626973.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000885864.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV001256073.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

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

From Genome-Nilou Lab, SCV001653482.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004016478.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 13, 2025