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NM_002609.4(PDGFRB):c.1681C>T (p.Arg561Cys) AND Myofibromatosis, infantile, 1

Germline classification:
Pathogenic (4 submissions)
Last evaluated:
May 31, 2018
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:
RCV000049264.30

Allele description [Variation Report for NM_002609.4(PDGFRB):c.1681C>T (p.Arg561Cys)]

NM_002609.4(PDGFRB):c.1681C>T (p.Arg561Cys)

Gene:
PDGFRB:platelet derived growth factor receptor beta [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q32
Genomic location:
Preferred name:
NM_002609.4(PDGFRB):c.1681C>T (p.Arg561Cys)
Other names:
NM_002609.3(PDGFRB):c.1681C>T(p.Arg561Cys)
HGVS:
  • NC_000005.10:g.150125571G>A
  • NG_023367.1:g.35289C>T
  • NM_001355016.2:c.1489C>T
  • NM_001355017.2:c.1198C>T
  • NM_002609.4:c.1681C>TMANE SELECT
  • NP_001341945.1:p.Arg497Cys
  • NP_001341946.1:p.Arg400Cys
  • NP_002600.1:p.Arg561Cys
  • NC_000005.9:g.149505134G>A
  • NM_002609.3:c.1681C>T
  • P09619:p.Arg561Cys
Protein change:
R400C; ARG561CYS
Links:
UniProtKB: P09619#VAR_069925; OMIM: 173410.0003; dbSNP: rs367543286
NCBI 1000 Genomes Browser:
rs367543286
Molecular consequence:
  • NM_001355016.2:c.1489C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001355017.2:c.1198C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002609.4:c.1681C>T - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
protein gain of function [Variation Ontology: 0040]

Condition(s)

Name:
Myofibromatosis, infantile, 1
Synonyms:
Myofibromatosis, juvenile
Identifiers:
MONDO: MONDO:0009227; MedGen: C4551572; Orphanet: 2591; OMIM: 228550

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000077520OMIM
no assertion criteria provided
Pathogenic
(Jun 6, 2013)
germlineliterature only

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

SCV000082631Center for Applied Genomics, Children's Hospital of Philadelphia
no classification provided
not providedgermlinenot provided

SCV000256759Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine
criteria provided, single submitter

(Cheung et al. (AJHG 2013))
Pathogenic
(Feb 12, 2013)
germlineresearch

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

SCV000803486SIB Swiss Institute of Bioinformatics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 31, 2018)
unknowncuration

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot provided1not providedliterature only
not providedunknownunknownnot providednot providednot providednot providednot providedcuration
not providedgermlineyes114not providednot providedyesresearch

Citations

PubMed

A recurrent PDGFRB mutation causes familial infantile myofibromatosis.

Cheung YH, Gayden T, Campeau PM, LeDuc CA, Russo D, Nguyen VH, Guo J, Qi M, Guan Y, Albrecht S, Moroz B, Eldin KW, Lu JT, Schwartzentruber J, Malkin D, Berghuis AM, Emil S, Gibbs RA, Burk DL, Vanstone M, Lee BH, Orchard D, et al.

Am J Hum Genet. 2013 Jun 6;92(6):996-1000. doi: 10.1016/j.ajhg.2013.04.026. Epub 2013 May 23.

PubMed [citation]
PMID:
23731537
PMCID:
PMC3675240

Mutations in PDGFRB cause autosomal-dominant infantile myofibromatosis.

Martignetti JA, Tian L, Li D, Ramirez MC, Camacho-Vanegas O, Camacho SC, Guo Y, Zand DJ, Bernstein AM, Masur SK, Kim CE, Otieno FG, Hou C, Abdel-Magid N, Tweddale B, Metry D, Fournet JC, Papp E, McPherson EW, Zabel C, Vaksmann G, Morisot C, et al.

Am J Hum Genet. 2013 Jun 6;92(6):1001-7. doi: 10.1016/j.ajhg.2013.04.024. Epub 2013 May 23.

PubMed [citation]
PMID:
23731542
PMCID:
PMC3675260
See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000077520.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In affected members of 4 unrelated families with infantile myofibromatosis-1 (IMF1; 228550), Cheung et al. (2013) identified a heterozygous c.1681C-T transition in the PDGFRB gene, resulting in an arg561-to-cys (R561C) substitution at a highly conserved residue. The families were of Chinese, European, French Canadian, and French origin, respectively. The mutation, which was identified by exome sequencing and confirmed by Sanger sequencing in the first 2 families, segregated with the phenotype in all families and was not found in several large control databases. Structural modeling indicated that the R561C mutation occurs in the cytoplasmic juxtamembrane (JM) region between the helical transmembrane segment and the kinase domain, and was predicted to compromise the autoinhibitory role of the JM domain, leading to increased kinase firing and promoting the formation of myofibromas in tissues with high PDGFRB signaling activity. In vitro functional studies were not performed.

Martignetti et al. (2013) identified a heterozygous R561C mutation in the PDGFRB gene in affected members from 7 unrelated families with autosomal dominant infantile myofibromatosis. The mutation, which was identified by exome sequencing and confirmed by Sanger sequencing, segregated with the disorder and was not found in several large control databases.

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

From Center for Applied Genomics, Children's Hospital of Philadelphia, SCV000082631.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot providednot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot provided1not providednot providednot providednot providednot providednot provided

From Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine, SCV000256759.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided11not providedyesresearch PubMed (1)

Description

This variant has been found in all 11 individuals with familial infantile myofibromatosis studied.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided11not provided4not provided

From SIB Swiss Institute of Bioinformatics, SCV000803486.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (5)

Description

This variant is interpreted as a Pathogenic, for Myofibromatosis, infantile, 1, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PM6 => Assumed de novo, but without confirmation of paternity and maternity (PMID:23731537). PP1-Strong => PP1 upgraded in strength to Strong (PMID:23731537) (PMID:23731542). PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS4-Moderate => Recurrent mutation found in multiple unrelated patients (PMID:23731537,23731542,28183292). PS3 => Well-established functional studies show a deleterious effect (PMID:26455322).

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

Last Updated: Sep 29, 2024