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NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg)

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
61
First in ClinVar:
Oct 1, 2013
Most recent Submission:
Mar 4, 2023
Last evaluated:
Feb 11, 2022
Accession:
VCV000013652.48
Variation ID:
13652
Description:
single nucleotide variant
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NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg)

Allele ID
28691
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3q26.32
Genomic location
3: 179234297 (GRCh38) GRCh38 UCSC
3: 178952085 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_006218.4:c.3140A>G MANE Select NP_006209.2:p.His1047Arg missense
NC_000003.12:g.179234297A>G
NC_000003.11:g.178952085A>G
... more HGVS
Protein change
H1047R
Other names
NM_006218.4(PIK3CA):c.3140A>G
COSM775
Canonical SPDI
NC_000003.12:179234296:A:G
Functional consequence
effect on protein activity [Variation Ontology VariO:0053]
gain_of_function_variant [Sequence Ontology SO:0002053]
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA123326
UniProtKB: P42336#VAR_026192
OMIM: 171834.0001
dbSNP: rs121913279
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 reviewed by expert panel Feb 11, 2022 RCV001836707.3
Pathogenic 5 criteria provided, multiple submitters, no conflicts Nov 11, 2019 RCV000024621.17
Pathogenic 5 criteria provided, multiple submitters, no conflicts Aug 3, 2022 RCV001092442.16
Pathogenic 2 criteria provided, single submitter Apr 19, 2019 RCV000201231.3
Pathogenic 1 criteria provided, single submitter - RCV000487449.2
Pathogenic 1 criteria provided, single submitter Oct 1, 2021 RCV001729349.2
Pathogenic 1 criteria provided, single submitter - RCV001526648.2
Segmental undergrowth associated with mainly venous malformation with capillary component
Pathogenic 1 criteria provided, single submitter Apr 6, 2021 RCV001705589.2
Segmental undergrowth associated with lymphatic malformation
Pathogenic 1 criteria provided, single submitter Apr 6, 2021 RCV001705590.2
Likely pathogenic 1 criteria provided, single submitter Nov 3, 2021 RCV001762045.2
Pathogenic 1 criteria provided, single submitter Feb 12, 2021 RCV001807727.2
Pathogenic 1 no assertion criteria provided Jun 24, 2012 RCV000014623.10
Pathogenic 1 no assertion criteria provided Jun 24, 2012 RCV000014624.9
Pathogenic/Likely pathogenic 2 no assertion criteria provided May 31, 2016 RCV000014626.10
Pathogenic 3 no assertion criteria provided Oct 2, 2014 RCV000014627.15
Pathogenic 1 no assertion criteria provided Jun 24, 2012 RCV000014628.10
Pathogenic 1 no assertion criteria provided Jun 24, 2012 RCV000014622.10
Pathogenic 3 no assertion criteria provided Dec 1, 2018 RCV000154516.8
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000425956.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000421855.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000422442.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000420562.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000430589.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000432543.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000426498.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000433127.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000419938.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000428372.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000426614.2
Pathogenic 1 no assertion criteria provided May 31, 2016 RCV000436234.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000437287.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000431232.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000442736.2
Pathogenic 1 no assertion criteria provided May 31, 2016 RCV000437153.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000432506.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000437782.2
Likely pathogenic 1 no assertion criteria provided Jul 14, 2015 RCV000438435.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000442731.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000442164.2
Likely pathogenic 1 no assertion criteria provided May 31, 2016 RCV000443546.2
MACRODACTYLY, SOMATIC
Pathogenic 1 no assertion criteria provided Jun 24, 2012 RCV000709691.4
Pathogenic 1 no assertion criteria provided Apr 30, 2019 RCV001255686.2
Pathogenic 1 no assertion criteria provided - RCV001327968.2
CEREBRAL CAVERNOUS MALFORMATIONS 4, SOMATIC
Pathogenic 1 no assertion criteria provided Jun 24, 2012 RCV001728091.2
Cerebrofacial Vascular Metameric Syndrome (CVMS)
Pathogenic 1 no assertion criteria provided Sep 30, 2021 RCV001730472.2
Pathogenic 1 no assertion criteria provided Jun 24, 2012 RCV002508124.1
Pathogenic 1 no assertion criteria provided - RCV003128082.1

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PIK3CA No evidence available No evidence available GRCh38
GRCh37
1033 1067

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Pathogenic
(Feb 11, 2022)
reviewed by expert panel
Method: curation
Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin: germline
ClinGen Brain Malformations Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV001949970.2
First in ClinVar: Oct 02, 2021
Last updated: Feb 20, 2022
Publications:
PubMed (3)
PubMed: 223706362998867723066039
Other databases
https://erepo.clinicalgenome.org… https://erepo.clinicalgenome.org/evrepo/ui/interpretation/f4d8f50e-a120-47e5-8b69-0a8921149fde
Comment:
The c.3140A>G (NM_006218.4) variant in PIK3CA is a missense variant predicted to cause substitution of (p.His1047Arg). This variant is present in one individual in gnomAD … (more)
Pathogenic
(Apr 19, 2019)
criteria provided, single submitter
Method: clinical testing
PIK3CA related overgrowth spectrum
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Biesecker Lab Rare Disease,National Institutes of Health
Accession: SCV000898478.1
First in ClinVar: Apr 28, 2019
Last updated: Apr 28, 2019
Clinical Features:
overgrowth (present)
Sex: male
Pathogenic
(Nov 11, 2019)
criteria provided, single submitter
Method: clinical testing
CLOVES syndrome
Affected status: yes
Allele origin: de novo
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001428754.1
First in ClinVar: Aug 16, 2020
Last updated: Aug 16, 2020
Number of individuals with the variant: 1
Pathogenic
(Oct 01, 2021)
criteria provided, single submitter
Method: clinical testing
CLAPO syndrome
Affected status: yes
Allele origin: unknown
Laboratory of Medical Genetics, National & Kapodistrian University of Athens
Accession: SCV001976965.1
First in ClinVar: Oct 16, 2021
Last updated: Oct 16, 2021
Publications:
PubMed (1)
PubMed: 34008892
Comment:
PS3, PM1, PM2, PM5, PP2, PP3, PP4, PP5
Pathogenic
(Feb 12, 2021)
criteria provided, single submitter
Method: clinical testing
Megalencephaly-capillary malformation-polymicrogyria syndrome
Affected status: no
Allele origin: somatic
Centogene AG - the Rare Disease Company
Accession: SCV002059601.1
First in ClinVar: Jan 15, 2022
Last updated: Jan 15, 2022
Pathogenic
(Aug 05, 2021)
criteria provided, single submitter
Method: clinical testing
Not provided
Affected status: yes
Allele origin: germline
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Accession: SCV002061476.2
First in ClinVar: Jan 22, 2022
Last updated: Feb 11, 2022
Comment:
PS4, PS3, PM2
Pathogenic
(Aug 03, 2022)
criteria provided, single submitter
Method: clinical testing
Not Provided
Affected status: yes
Allele origin: germline
GeneDx
Accession: SCV002559314.2
First in ClinVar: Aug 15, 2022
Last updated: Mar 04, 2023
Comment:
Reported as a somatic variant in various tumor samples (Campbell et al., 2004; Li et al., 2005); Published functional studies demonstrate increased lipid kinase activity … (more)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Rosette-forming glioneuronal tumor
Affected status: yes
Allele origin: somatic
Donald Williams Parsons Laboratory,Baylor College of Medicine
Additional submitter:
Sharon E. Plon Laboratory,Baylor College of Medicine
Study: CSER-BASIC3
Accession: SCV000292259.2
First in ClinVar: Apr 28, 2017
Last updated: Apr 28, 2017
Comment:
The c.3140A>G missense mutation (p.H1047R) identified in exon 21 of PIK3CA is the most frequently-observed PIK3CA hotspot alteration in human cancers , including high grade … (more)
Publications:
PubMed (1)
PubMed: 27626068
Clinical Features:
Rosette-forming glioneuronal tumor (present)
Zygosity: 1 Single Heterozygote
Age: 10-19 years
Sex: female
Ethnicity/Population group: African American
Tissue: frozen tumor sample : Rosette-forming glioneuronal tumor of the fourth ventricle
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
CLOVES syndrome
Affected status: yes
Allele origin: unknown
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Study: Clinvar_gadteam_Clinical_exome_analysis_3
Accession: SCV000803841.1
First in ClinVar: Apr 21, 2017
Last updated: Apr 21, 2017
Pathogenic
(Oct 23, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
(Autosomal unknown)
Affected status: yes
Allele origin: germline
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001446687.1
First in ClinVar: Nov 28, 2020
Last updated: Nov 28, 2020
Clinical Features:
Overgrowth (present) , Congenital macrodactylia (present)
Sex: female
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Congenital macrodactylia
Affected status: yes
Allele origin: somatic
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV001737079.1
First in ClinVar: Jun 19, 2021
Last updated: Jun 19, 2021
Pathogenic
(Apr 06, 2021)
criteria provided, single submitter
Method: clinical testing
Segmental undergrowth associated with lymphatic malformation
Affected status: yes
Allele origin: somatic
Institute of Medical and Molecular Genetics,Hospital Universitario La Paz
Accession: SCV001934209.1
First in ClinVar: Sep 25, 2021
Last updated: Sep 25, 2021
Number of individuals with the variant: 2
Clinical Features:
Limb undergrowth (present) , Lymphangioma (present)
Pathogenic
(Apr 06, 2021)
criteria provided, single submitter
Method: clinical testing
Segmental undergrowth associated with mainly venous malformation with capillary component
Affected status: yes
Allele origin: somatic
Institute of Medical and Molecular Genetics,Hospital Universitario La Paz
Accession: SCV001934211.1
First in ClinVar: Sep 25, 2021
Last updated: Sep 25, 2021
Number of individuals with the variant: 1
Clinical Features:
Limb undergrowth (present) , Venous malformation (present) , Capillary malformation (present)
Likely pathogenic
(Nov 03, 2021)
criteria provided, single submitter
Method: clinical testing
Familial cancer of breast
Affected status: yes
Allele origin: germline
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV002009609.1
First in ClinVar: Nov 06, 2021
Last updated: Nov 06, 2021
Pathogenic
(Sep 20, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: yes
Allele origin: somatic
Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital
Accession: SCV002525705.1
First in ClinVar: Jun 11, 2022
Last updated: Jun 11, 2022
Comment:
This variant substitutes the histidine with arginine at position 1047 within the PIK3CA kinase domain. This is a recurrent pathogenic variant. Several unrelated individuals with … (more)

Observation 1:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present)

Observation 2:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present)

Observation 3:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present)

Observation 4:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present)

Observation 5:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present)

Observation 6:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present)

Observation 7:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present) , Overgrowth (present)

Observation 8:

Number of individuals with the variant: 1
Clinical Features:
Venous malformation (present)

Observation 9:

Number of individuals with the variant: 1
Clinical Features:
Neoplasm (present) , Vascular skin abnormality (present) , Hemangioma (present)

Observation 10:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present)

Observation 11:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present)

Observation 12:

Number of individuals with the variant: 1
Clinical Features:
Congenital macrodactylia (present) , Macrodactyly of finger (present)

Observation 13:

Number of individuals with the variant: 1

Observation 14:

Number of individuals with the variant: 1

Observation 15:

Number of individuals with the variant: 1

Observation 16:

Number of individuals with the variant: 1

Observation 17:

Number of individuals with the variant: 1

Observation 18:

Number of individuals with the variant: 1
Clinical Features:
Abnormal lymphatic vessel morphology (present)
Pathogenic
(Jun 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: yes
Allele origin: germline
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001248958.13
First in ClinVar: May 12, 2020
Last updated: Jan 21, 2023
Number of individuals with the variant: 2
Pathogenic
(Aug 05, 2010)
no assertion criteria provided
Method: clinical testing
Ovarian Cancer
Affected status: not provided
Allele origin: somatic
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000204187.1
First in ClinVar: Jan 31, 2015
Last updated: Jan 31, 2015
Number of individuals with the variant: 1
Pathogenic
(Apr 01, 2015)
no assertion criteria provided
Method: clinical testing
PIK3CA Related Overgrowth Spectrum
Affected status: yes
Allele origin: somatic
Genomics and Pathology Services,Washington University in St.Louis
Accession: SCV000255984.1
First in ClinVar: Oct 22, 2015
Last updated: Oct 22, 2015

Observation 1:

Indication for testing: Lipoma
Tissue: FFPE

Observation 2:

Indication for testing: Polydactyly; Syndactyly; Other specified congenital abnormalities
Tissue: FFPE
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Ovarian serous cystadenocarcinoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504107.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Neoplasm of uterine cervix
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504108.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Uterine carcinosarcoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504109.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Breast neoplasm
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504110.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (10)
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Pathogenic
(Oct 02, 2014)
no assertion criteria provided
Method: literature only
Non-small cell lung carcinoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504111.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (11)
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Brainstem glioma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504112.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Neoplasm of the large intestine
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504113.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (12)
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Malignant melanoma of skin
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504114.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Malignant neoplasm of body of uterus
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504115.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Carcinoma of esophagus
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504116.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Pancreatic adenocarcinoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504117.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Adrenal cortex carcinoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504118.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(Jul 14, 2015)
no assertion criteria provided
Method: literature only
Neoplasm
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504119.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 25157968
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Pathogenic
(Oct 02, 2014)
no assertion criteria provided
Method: literature only
Neoplasm of ovary
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504120.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (2)
PubMed: 1564737022271473
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Transitional cell carcinoma of the bladder
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504121.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Hepatocellular carcinoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504122.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Medulloblastoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504123.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Neoplasm of brain
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504124.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Prostate adenocarcinoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504125.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
None
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504126.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Renal cell carcinoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504127.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Gastric adenocarcinoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504128.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Squamous cell lung carcinoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504129.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
None
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504130.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Likely pathogenic
(May 31, 2016)
no assertion criteria provided
Method: literature only
Glioblastoma
(Somatic mutation)
Affected status: yes
Allele origin: somatic
Database of Curated Mutations (DoCM)
Accession: SCV000504131.1
First in ClinVar: Mar 08, 2017
Last updated: Mar 08, 2017
Publications:
PubMed (1)
PubMed: 26619011
Other databases
http://docm.genome.wustl.edu/var… http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G
Pathogenic
(Dec 01, 2018)
no assertion criteria provided
Method: research
Neoplasm of ovary
Affected status: yes
Allele origin: somatic
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne
Accession: SCV000923968.1
First in ClinVar: Jun 17, 2019
Last updated: Jun 17, 2019
Pathogenic
(Apr 30, 2019)
no assertion criteria provided
Method: research
Lip and oral cavity carcinoma
Affected status: yes
Allele origin: somatic
Institute of Medical Sciences, Banaras Hindu University
Accession: SCV001432251.1
First in ClinVar: Sep 18, 2020
Last updated: Sep 18, 2020
Publications:
PubMed (1)
PubMed: 31775759
Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
BREAST CANCER, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV000034877.6
First in ClinVar: Apr 04, 2013
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
OVARIAN CANCER, EPITHELIAL, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV000034878.6
First in ClinVar: Apr 04, 2013
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
COLORECTAL CANCER, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV000034879.6
First in ClinVar: Apr 04, 2013
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
GASTRIC CANCER, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV000034880.6
First in ClinVar: Apr 04, 2013
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
HEPATOCELLULAR CARCINOMA, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV000034881.6
First in ClinVar: Apr 04, 2013
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
NONSMALL CELL LUNG CANCER, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV000034882.6
First in ClinVar: Apr 04, 2013
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
KERATOSIS, SEBORRHEIC, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV000034883.6
First in ClinVar: Apr 04, 2013
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
CONGENITAL LIPOMATOUS OVERGROWTH, VASCULAR MALFORMATIONS, AND EPIDERMAL NEVI, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV000050487.6
First in ClinVar: Apr 04, 2013
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
MACRODACTYLY, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV000839591.3
First in ClinVar: Oct 14, 2018
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Sep 30, 2021)
no assertion criteria provided
Method: clinical testing
Cerebrofacial Vascular Metameric Syndrome (CVMS)
(Somatic mutation)
Affected status: yes
Allele origin: somatic
James Bennett Lab,Seattle Childrens Research Institute
Accession: SCV001960168.1
First in ClinVar: Oct 21, 2021
Last updated: Oct 21, 2021
Publications:
PubMed (3)
PubMed: 266270072265854431536475
Pathogenic
(Aug 05, 2010)
no assertion criteria provided
Method: clinical testing
Non-Small Cell Lung Cancer
Affected status: not provided
Allele origin: somatic
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000199905.1
First in ClinVar: Jan 31, 2015
Last updated: Jan 31, 2015
Number of individuals with the variant: 12
Pathogenic
(-)
no assertion criteria provided
Method: provider interpretation
Abnormality of cardiovascular system morphology
Affected status: yes
Allele origin: somatic
MAGI's Lab - Research,MAGI Group
Accession: SCV001437644.1
First in ClinVar: Mar 18, 2021
Last updated: Mar 18, 2021

Observation 1:

Observation 2:

Observation 3:

Observation 4:

Observation 5:

Pathogenic
(Jun 24, 2012)
no assertion criteria provided
Method: literature only
CEREBRAL CAVERNOUS MALFORMATIONS 4, SOMATIC
Affected status: not provided
Allele origin: somatic
OMIM
Accession: SCV001976535.1
First in ClinVar: Oct 08, 2021
Last updated: Oct 08, 2021
Publications:
PubMed (10)
Comment on evidence:
Colorectal Cancer In a relatively high frequency of colorectal cancers (114500), Samuels et al. (2004) identified a his1047-to-arg (H1047R) mutation in the PIK3CA gene; in … (more)
Pathogenic
(Jun 02, 2022)
no assertion criteria provided
Method: clinical testing
CLOVES syndrome
Affected status: yes
Allele origin: germline
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein
Accession: SCV002583480.1
First in ClinVar: Oct 15, 2022
Last updated: Oct 15, 2022
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
Breast carcinoma
Affected status: yes
Allele origin: somatic
Medical Oncology,Institut Jules Bordet
Accession: SCV003803732.1
First in ClinVar: Feb 25, 2023
Last updated: Feb 25, 2023
Publications:
PubMed (3)
PubMed: 205933142237063627126994
Sex: female
not provided
(-)
no assertion provided
Method: literature only
CLOVES syndrome
Affected status: not provided
Allele origin: unknown
GeneReviews
Accession: SCV000086944.2
First in ClinVar: Oct 01, 2013
Last updated: Oct 01, 2022
Publications:
PubMed (3)
PubMed: 226585442272922223946963

Functional evidence

Help
Functional consequence Method Result Submitter Supporting information
effect on protein activity
Biesecker Lab Rare Disease,National Institutes of Health
Accession: SCV000898478.1
Submitted: (Apr 25, 2019)
Evidence details
gain_of_function_variant
James Bennett Lab,Seattle Childrens Research Institute
Accession: SCV001960168.1
Submitted: (Oct 19, 2021)
Evidence details
Publications
PubMed (3)

Citations for this variant

Help
Title Author Journal Year Link
PIK3CA-Related Overgrowth Spectrum. Adam MP - 2022 PMID: 23946963
PIK3CA-Related Overgrowth Spectrum. Adam MP - 2022 BookShelf: NBK153722
Somatic PIK3CA Mutations in Sporadic Cerebral Cavernous Malformations. Peyre M The New England journal of medicine 2021 PMID: 34496175
Phenotype-driven variant filtration strategy in exome sequencing toward a high diagnostic yield and identification of 85 novel variants in 400 patients with rare Mendelian disorders. Marinakis NM American journal of medical genetics. Part A 2021 PMID: 34008892
Mutational spectrum of tobacco associated oral squamous carcinoma and its therapeutic significance. Batta N World journal of surgical oncology 2019 PMID: 31775759
Genotype correlates with clinical severity in PIK3CA-associated lymphatic malformations. Zenner K JCI insight 2019 PMID: 31536475
Molecular heterogeneity of the cerebriform connective tissue nevus in mosaic overgrowth syndromes. Keppler-Noreuil KM Cold Spring Harbor molecular case studies 2019 PMID: 31371346
PIK3CA c.3140A>G mutation in a patient with suspected Proteus Syndrome: a case report. Valentini V Clinical case reports 2018 PMID: 29988677
A Phase Ib Study of Alpelisib (BYL719), a PI3Kα-Specific Inhibitor, with Letrozole in ER+/HER2- Metastatic Breast Cancer. Mayer IA Clinical cancer research : an official journal of the American Association for Cancer Research 2017 PMID: 27126994
Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle. Lin FY Cold Spring Harbor molecular case studies 2016 PMID: 27626068
Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. Chang MT Nature biotechnology 2016 PMID: 26619011
Identification of Variant-Specific Functions of PIK3CA by Rapid Phenotyping of Rare Mutations. Dogruluk T Cancer research 2015 PMID: 26627007
Reactivation of multipotency by oncogenic PIK3CA induces breast tumour heterogeneity. Van Keymeulen A Nature 2015 PMID: 26266985
PIK3CA(H1047R) induces multipotency and multi-lineage mammary tumours. Koren S Nature 2015 PMID: 26266975
Prospective enterprise-level molecular genotyping of a cohort of cancer patients. MacConaill LE The Journal of molecular diagnostics : JMD 2014 PMID: 25157968
Somatic gain-of-function mutations in PIK3CA in patients with macrodactyly. Rios JJ Human molecular genetics 2013 PMID: 23100325
PIK3CA mutation H1047R is associated with response to PI3K/AKT/mTOR signaling pathway inhibitors in early-phase clinical trials. Janku F Cancer research 2013 PMID: 23066039
Conditional activation of Pik3ca(H1047R) in a knock-in mouse model promotes mammary tumorigenesis and emergence of mutations. Yuan W Oncogene 2013 PMID: 22370636
Mosaic overgrowth with fibroadipose hyperplasia is caused by somatic activating mutations in PIK3CA. Lindhurst MJ Nature genetics 2012 PMID: 22729222
Somatic mosaic activating mutations in PIK3CA cause CLOVES syndrome. Kurek KC American journal of human genetics 2012 PMID: 22658544
PI3K/AKT/mTOR inhibitors in patients with breast and gynecologic malignancies harboring PIK3CA mutations. Janku F Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2012 PMID: 22271473
Phase I, dose-escalation study of BKM120, an oral pan-Class I PI3K inhibitor, in patients with advanced solid tumors. Bendell JC Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2012 PMID: 22162589
Phosphatidylinositide-3-kinase inhibitors: addressing questions of isoform selectivity and pharmacodynamic/predictive biomarkers in early clinical trials. Clarke PA Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2012 PMID: 22162582
The selective class I PI3K inhibitor CH5132799 targets human cancers harboring oncogenic PIK3CA mutations. Tanaka H Clinical cancer research : an official journal of the American Association for Cancer Research 2011 PMID: 21558396
Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors. Sequist LV Science translational medicine 2011 PMID: 21430269
Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis. De Roock W The Lancet. Oncology 2010 PMID: 20619739
Structural effects of oncogenic PI3Kα mutations. Gabelli SB Current topics in microbiology and immunology 2010 PMID: 20593314
Predictive biomarkers of sensitivity to the phosphatidylinositol 3' kinase inhibitor GDC-0941 in breast cancer preclinical models. O'Brien C Clinical cancer research : an official journal of the American Association for Cancer Research 2010 PMID: 20453058
PIK3CA mutations predict local recurrences in rectal cancer patients. He Y Clinical cancer research : an official journal of the American Association for Cancer Research 2009 PMID: 19903786
A novel dual PI3Kalpha/mTOR inhibitor PI-103 with high antitumor activity in non-small cell lung cancer cells. Zou ZQ International journal of molecular medicine 2009 PMID: 19513541
PIK3CA mutations are not a major determinant of resistance to the epidermal growth factor receptor inhibitor cetuximab in metastatic colorectal cancer. Prenen H Clinical cancer research : an official journal of the American Association for Cancer Research 2009 PMID: 19366826
PIK3CA mutations in colorectal cancer are associated with clinical resistance to EGFR-targeted monoclonal antibodies. Sartore-Bianchi A Cancer research 2009 PMID: 19223544
Effective use of PI3K and MEK inhibitors to treat mutant Kras G12D and PIK3CA H1047R murine lung cancers. Engelman JA Nature medicine 2008 PMID: 19029981
Breast tumor cells with PI3K mutation or HER2 amplification are selectively addicted to Akt signaling. She QB PloS one 2008 PMID: 18725974
An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer. Stemke-Hale K Cancer research 2008 PMID: 18676830
Oncogenic PIK3CA mutations occur in epidermal nevi and seborrheic keratoses with a characteristic mutation pattern. Hafner C Proceedings of the National Academy of Sciences of the United States of America 2007 PMID: 17673550
PIK3CA mutation status in Japanese lung cancer patients. Kawano O Lung cancer (Amsterdam, Netherlands) 2006 PMID: 16930767
Allelic dilution obscures detection of a biologically significant resistance mutation in EGFR-amplified lung cancer. Engelman JA The Journal of clinical investigation 2006 PMID: 16906227
PIK3CA mutations correlate with hormone receptors, node metastasis, and ERBB2, and are mutually exclusive with PTEN loss in human breast carcinoma. Saal LH Cancer research 2005 PMID: 15805248
Phosphatidylinositol 3-kinase mutations identified in human cancer are oncogenic. Kang S Proceedings of the National Academy of Sciences of the United States of America 2005 PMID: 15647370
PIK3CA gene is frequently mutated in breast carcinomas and hepatocellular carcinomas. Lee JW Oncogene 2005 PMID: 15608678
Mutation of the PIK3CA gene in ovarian and breast cancer. Campbell IG Cancer research 2004 PMID: 15520168
The PIK3CA gene is mutated with high frequency in human breast cancers. Bachman KE Cancer biology & therapy 2004 PMID: 15254419
High frequency of mutations of the PIK3CA gene in human cancers. Samuels Y Science (New York, N.Y.) 2004 PMID: 15016963
http://docm.genome.wustl.edu/variants/ENST00000263967:c.3140A>G - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/f4d8f50e-a120-47e5-8b69-0a8921149fde - - - -

Text-mined citations for rs121913279...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Mar 26, 2023