NM_002529.3(NTRK1):c.2046+1G>T AND Hereditary insensitivity to pain with anhidrosis

Clinical significance:Likely pathogenic (Last evaluated: Jul 17, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_002529.3(NTRK1):c.2046+1G>T]


NTRK1:neurotrophic receptor tyrosine kinase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000001.11:g.156879363G>T
  • NG_007493.1:g.68614G>T
  • NM_001007792.1:c.1938+1G>T
  • NM_001012331.1:c.2028+1G>T
  • NM_002529.3:c.2046+1G>T
  • LRG_261t1:c.1938+1G>T
  • LRG_261t2:c.2028+1G>T
  • LRG_261t3:c.2046+1G>T
  • LRG_261:g.68614G>T
  • NC_000001.10:g.156849155G>T
dbSNP: rs1452844753
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001007792.1:c.1938+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001012331.1:c.2028+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_002529.3:c.2046+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]


Hereditary insensitivity to pain with anhidrosis (CIPA)
FAMILIAL DYSAUTONOMIA, TYPE II; Insensitivity to pain, congenital, with anhidrosis; Neuropathy, congenital sensory, with anhidrosis; See all synonyms [MedGen]
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)
SCV000626954Invitaecriteria provided, single submitter
Likely pathogenic
(Jul 17, 2017)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing



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):240-242.

PubMed [citation]

Details of each submission

From Invitae, SCV000626954.1

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


This sequence change affects a donor splice site in intron 14 of the NTRK1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with NTRK1-related disease. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in NTRK1 are known to be pathogenic (PMID: 10982191). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Apr 17, 2020

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