NM_212472.2(PRKAR1A):c.349-5T>C AND Carney complex, type 1

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: May 28, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000704003.4

Allele description [Variation Report for NM_212472.2(PRKAR1A):c.349-5T>C]

NM_212472.2(PRKAR1A):c.349-5T>C

Gene:
PRKAR1A:protein kinase cAMP-dependent type I regulatory subunit alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q24.2
Genomic location:
Preferred name:
NM_212472.2(PRKAR1A):c.349-5T>C
HGVS:
  • NC_000017.11:g.68523720T>C
  • NG_007093.3:g.115098T>C
  • NM_001276289.1:c.349-5T>C
  • NM_001276290.1:c.349-5T>C
  • NM_001278433.1:c.349-5T>C
  • NM_001369389.1:c.349-5T>C
  • NM_001369390.1:c.349-5T>C
  • NM_002734.4:c.349-5T>C
  • NM_212471.2:c.349-5T>C
  • NM_212472.2:c.349-5T>C
  • LRG_514t1:c.349-5T>C
  • LRG_514t2:c.349-5T>C
  • LRG_514:g.115098T>C
  • NC_000017.10:g.66519861T>C
Links:
dbSNP: rs1456043929
NCBI 1000 Genomes Browser:
rs1456043929
Molecular consequence:
  • NM_001276289.1:c.349-5T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276290.1:c.349-5T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001278433.1:c.349-5T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369389.1:c.349-5T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001369390.1:c.349-5T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_002734.4:c.349-5T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_212471.2:c.349-5T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_212472.2:c.349-5T>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Carney complex, type 1 (CNC1)
Synonyms:
CARNEY MYXOMA-ENDOCRINE COMPLEX
Identifiers:
MONDO: MONDO:0008057; MedGen: C2607929; Orphanet: 1359; OMIM: 160980

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000832935Invitaecriteria provided, single submitter
Uncertain significance
(May 4, 2019)
germlineclinical testing

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

SCV001140823Mendelicscriteria provided, single submitter
Likely benign
(May 28, 2019)
unknownclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000832935.3

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

Description

This sequence change falls in intron 3 of the PRKAR1A gene. It does not directly change the encoded amino acid sequence of the PRKAR1A protein. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PRKAR1A-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. 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

From Mendelics, SCV001140823.1

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

Last Updated: Apr 12, 2021

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