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NM_006218.4(PIK3CA):c.1624G>A (p.Glu542Lys) AND CLAPO syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 8, 2012
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000709693.14

Allele description [Variation Report for NM_006218.4(PIK3CA):c.1624G>A (p.Glu542Lys)]

NM_006218.4(PIK3CA):c.1624G>A (p.Glu542Lys)

Gene:
PIK3CA:phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q26.32
Genomic location:
Preferred name:
NM_006218.4(PIK3CA):c.1624G>A (p.Glu542Lys)
Other names:
NM_006218.3(PIK3CA):c.1624G>A; NM_006218.4(PIK3CA):c.1624G>A
HGVS:
  • NC_000003.12:g.179218294G>A
  • NG_012113.2:g.74772G>A
  • NM_006218.4:c.1624G>AMANE SELECT
  • NP_006209.2:p.Glu542Lys
  • LRG_310t1:c.1624G>A
  • LRG_310:g.74772G>A
  • NC_000003.11:g.178936082G>A
  • NM_006218.2:c.1624G>A
  • NM_006218.3:c.1624G>A
  • P42336:p.Glu542Lys
  • NM_006218.2:c.1625G>A
Protein change:
E542K; GLU542LYS
Links:
UniProtKB: P42336#VAR_026173; OMIM: 171834.0009; dbSNP: rs121913273
NCBI 1000 Genomes Browser:
rs121913273
Molecular consequence:
  • NM_006218.4:c.1624G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
gain_of_function_variant [Sequence Ontology: SO:0002053]

Condition(s)

Name:
CLAPO syndrome
Synonyms:
LOPEZ-GUTIERREZ SYNDROME; Capillary malformation of the lower lip, lymphatic malformation of face and neck, asymmetry of face and limbs, and partial/generalized overgrowth
Identifiers:
MONDO: MONDO:0013125; MedGen: C2751313; Orphanet: 168984; OMIM: 613089

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000839593OMIM
no assertion criteria provided
Pathogenic
(Jun 8, 2012)
somaticliterature only

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedsomaticnot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Somatic mosaic activating mutations in PIK3CA cause CLOVES syndrome.

Kurek KC, Luks VL, Ayturk UM, Alomari AI, Fishman SJ, Spencer SA, Mulliken JB, Bowen ME, Yamamoto GL, Kozakewich HP, Warman ML.

Am J Hum Genet. 2012 Jun 8;90(6):1108-15. doi: 10.1016/j.ajhg.2012.05.006. Epub 2012 May 31.

PubMed [citation]
PMID:
22658544
PMCID:
PMC3370283

CLAPO syndrome: identification of somatic activating PIK3CA mutations and delineation of the natural history and phenotype.

Rodriguez-Laguna L, Ibañez K, Gordo G, Garcia-Minaur S, Santos-Simarro F, Agra N, Vallespín E, Fernández-Montaño VE, Martín-Arenas R, Del Pozo Á, González-Pecellín H, Mena R, Rueda-Arenas I, Gomez MV, Villaverde C, Bustamante A, Ayuso C, Ruiz-Perez VL, Nevado J, Lapunzina P, Lopez-Gutierrez JC, Martinez-Glez V.

Genet Med. 2018 Aug;20(8):882-889. doi: 10.1038/gim.2017.200. Epub 2018 Feb 15.

PubMed [citation]
PMID:
29446767
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000839593.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

CLOVE Syndrome

In a 14-year-old girl and an unrelated 1-year-old boy with CLOVE syndrome (612918), Kurek et al. (2012) identified somatic mosaicism for a 1624G-A transition in the PIK3CA gene, resulting in a glu542-to-lys (E542K) substitution that was present in affected tissues from multiple embryonic lineages with a mutant allele frequency ranging from 6 to 13%.

CLAPO Syndrome

In tissue from a lower lip capillary malformation (CM) from a 2-year-old female patient (P10) with CLAPO syndrome (613089), Rodriguez-Laguna et al. (2018) identified a c.1624G-A transition (c.1624G-A, NM_006218.2) in the PIK3CA gene that resulted in a glu542-to-lys (E542K) mutation in the helical domain. The mutation was present at an allele frequency of 10% by deep sequencing, was present in 999 samples from the Catalogue of Somatic Mutations in Cancer (COSMIC) database, and had been previously reported in 44 patients with vascular overgrowth disorders. Functional studies were not performed.

Cerebral Cavernous Malformations 4

In samples of cerebral cavernous malformations-4 (CCM4; 619538) from 16 unrelated patients with sporadic occurrence of the disease, Peyre et al. (2021) identified a somatic E542K mutation in the PIK3CA gene. The mutation was found by targeted DNA sequencing. PIK3CA-mutant CCMs showed increased phosphorylation of myosin light chain and activation of the PI3K-AKT-mTOR pathway, consistent with an activating mutation.

Hemifacial Myohyperplasia

In 2 patients (patients 3 and 4) with hemifacial myohyperplasia (HFMH; 606773), Bayard et al. (2023) identified mosaicism for the E542K mutation in the PIK3CA gene. Bayard et al. (2023) performed genotyping on muscle biopsies from affected regions and found a mutation burden of 12% in patient 3 and 21% in patient 4.

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

Last Updated: Nov 10, 2024