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NM_002730.4(PRKACA):c.409G>A (p.Gly137Arg) AND Cardioacrofacial dysplasia 1

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
May 9, 2022
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:
RCV001271119.4

Allele description [Variation Report for NM_002730.4(PRKACA):c.409G>A (p.Gly137Arg)]

NM_002730.4(PRKACA):c.409G>A (p.Gly137Arg)

Gene:
PRKACA:protein kinase cAMP-activated catalytic subunit alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.12
Genomic location:
Preferred name:
NM_002730.4(PRKACA):c.409G>A (p.Gly137Arg)
HGVS:
  • NC_000019.10:g.14100836C>T
  • NG_029699.1:g.21912G>A
  • NM_001304349.2:c.637G>A
  • NM_002730.4:c.409G>AMANE SELECT
  • NM_207518.3:c.385G>A
  • NP_001291278.1:p.Gly213Arg
  • NP_002721.1:p.Gly137Arg
  • NP_997401.1:p.Gly129Arg
  • NC_000019.9:g.14211648C>T
  • NM_002730.3:c.409G>A
Protein change:
G129R; GLY137ARG
Links:
OMIM: 601639.0002; dbSNP: rs148280386
NCBI 1000 Genomes Browser:
rs148280386
Molecular consequence:
  • NM_001304349.2:c.637G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002730.4:c.409G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_207518.3:c.385G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Cardioacrofacial dysplasia 1
Identifiers:
MONDO: MONDO:0030876; MedGen: C5436885; OMIM: 619142

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001451963OMIM
no assertion criteria provided
Pathogenic
(Dec 28, 2020)
germlineliterature only

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

SCV0023188573billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 22, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV002507149Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(May 9, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Germline and Mosaic Variants in PRKACA and PRKACB Cause a Multiple Congenital Malformation Syndrome.

Palencia-Campos A, Aoto PC, Machal EMF, Rivera-Barahona A, Soto-Bielicka P, Bertinetti D, Baker B, Vu L, Piceci-Sparascio F, Torrente I, Boudin E, Peeters S, Van Hul W, Huber C, Bonneau D, Hildebrand MS, Coleman M, Bahlo M, Bennett MF, Schneider AL, Scheffer IE, Kibæk M, et al.

Am J Hum Genet. 2020 Nov 5;107(5):977-988. doi: 10.1016/j.ajhg.2020.09.005. Epub 2020 Oct 14.

PubMed [citation]
PMID:
33058759
PMCID:
PMC7675002

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From OMIM, SCV001451963.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In affected individuals from 3 unrelated families from Egypt (family 1), Belgium (family 2), and Italy (family 3) with cardioacrofacial dysplasia (CAFD1; 619142), Palencia-Campos et al. (2020) identified heterozygosity or mosaicism for a c.409G-A transition (c.409G-A, NM_002730.4) in the PRKACA gene, resulting in a gly137-to-arg (G137R) substitution at a highly conserved residue at a tethering surface that interacts with regulatory proteins. The G137R variant was not found in the gnomAD database. In the Egyptian proband (P1), the variant was mosaic, with a variant allele fraction (VAF) of 0.28; his 2 affected offspring for whom DNA was available carried the variant in heterozygous state. The unaffected father of the Belgian proband (P2) was mosaic for G137R (VAF 0.16), but the variant was germline-transmitted in P2 (VAF 0.55) and her affected fetus (VAF 0.46). The mutation was found to have occurred de novo in the Italian proband (P3). Fluorescence polarization assays of purified holoenzymes showed greater sensitivity of the mutant holoenzyme to lower cAMP concentrations than with wildtype protein, and PepTag assay in transfected HEK293 cells showed increased kinase activity with the G137R mutant at low cAMP concentrations compared to wildtype protein. Analysis of hedgehog (see 600725) pathway signaling in retrotransduced NIH 3T3 cells after stimulation with the SMO (601500) agonist SAG revealed that the G137R mutant impairs SAG-mediated inactivation of PKA.

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

From 3billion, SCV002318857.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

The variant has been previously reported as de novo in a similarly affected individual (PMID: 33058759). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 33058759). A missense variant is a common mechanism. It is not observed in the gnomAD v2.1.1 dataset. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV002507149.1

#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: Feb 25, 2023