Genetic Information

Gene & Transcript Details

Gene
PIK3CA
Transcript
NM_006218.2 MANE Select
Total Exons
Reference Sequence
NC_000003.11
Alternative Transcripts
IDStatusDetails
NM_006218.2 Alternative 3724 nt | 158–3364
NM_006218.3 Alternative 9104 nt | 158–3364
NM_006218.4 MANE Select 9259 nt | 324–3530

Variant Details

HGVS Notation
NM_006218.2:c.3140A>G
Protein Change
H1047R
Location
Exon 21 (Exon 21 of )
21
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.000403 in 100,000
Extremely Rare
ACMG Criteria Applied PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).

ClinVar

Open
Classification
Likely Pathogenic
2 publications
Publications List
PMID: 34008892

PS3, PM1, PM2, PM5, PP2, PP3, PP4, PP5

PMID: 22370636

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 v2.1.1 (PM2_Supporting). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4_VS; PMIDs: 27191687, 28328134, 25292196, 22729222, 25424831, 465 entries in COSMIC, Segmental overgrowth or vascular malformation of a limb or region of the body, present in patient derived cell lines). 60 independent Ba/F3 and 57 independent MCF10A experiments showed this variant has a proliferative effect indicating that this variant impacts protein function (PMID:29533785 ) (PS3_Moderate). This variant resides within the kinase domain of PIK3CA that is defined as a critical functional domain by the ClinGen BMEP (PMIDs: 26637981, 24459181, 27631024) (PM1_Supporting). PIK3CA, in which the variant was identified, is defined by the ClinGen Brain Malformations Expert Panel as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). Testing of unaffected and affected tissue show variable allelic fractions consistent with a post-zygotic event (PS2_Moderate; PMID: 25424831). In summary, this variant meets the criteria to be classified as Pathogenic for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: PM2_P, PS4_VS, PS3_M, PM1_P, PP2, PS2_M; 15 points (VCEP specifications version 1; Approved: 1/31/2021)

Clinical Statement

"This variant has been reported in ClinVar as Pathogenic (25 clinical laboratories) and as Likely pathogenic (3 clinical laboratories) and as Pathogenic by ClinGen Brain Malformations Variant Curation Expert Panel expert panel."

COSMIC Somatic Evidence

Open
COSMIC ID
COSM775
Recurrence
3819 occurrences
PM1 Criteria
Applied
COSMIC Database Preview
COSMIC Preview
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Functional Impact & Domains

Functional Domain

Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene PIK3CA.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: PIK3CAH1047RPIK3CAH1047RSomaticNCBI Gene:5290|Show additional gene information Variant OverviewPIK3CA, the catalytic subunit of PI3-kinase, is frequently mutated in a diverse range of cancers including breast, endometrial and cervical cancers.The PIK3CA H1047R mutation is known to be oncogenic.Hide mutation effect description The PIK3CA H1047R mutation is located in the kinase domain in exon 21 of the protein (PMID: 16341083, 17376864, 22120714). This mutation has been found in various cancers, including breast, head and neck, lung, colorectal and endometrial cancers (PMID: 27126994, 25631445, 23787421, 25079552, 22960745, 22941189, 17376864, 23636398). Expression of this mutation in chicken embryonic fibroblasts, Ba/F3 cells and MCF10A breast cells and in a transgenic mouse model demonstrated that it is activating as measured by increased kinase activity, downstream pathway activation, cytokine- and factor-independent proliferation, colony growth in soft agar, invasion and in vivo glioblastoma tumor burden compared to wildtype PIK3CA (PMID: 17376864, 26627007, 16432179, 16322248, 31996845). Genetically engineered mouse models have shown that the PIK3CA H1047R mutation promotes tumor formation in breast, colon, ovarian and lung cancer and malignant mesothelioma (PMID: 22370636, 23940356, 22214849, 21822287, 21324922, 19029981, 31911549). Mutations at this position are predicted to constitutively activate the catalytic subunit of PI3K (p110α) by exposing the catalytic loop towards the plasma membrane where its substrate, PIP2, is found (PMID: 17376864, 20593314). Patients with breast cancer harboring this mutation achieved partial response (n=2) or stable disease (n=1) following treatment with the PI3Kα inhibitor, alpelisib (PMID: 27126994). In a phase III trial of palbociclib/fulvestrant for ER+, HER2− advanced breast cancer that had previously progressed on endocrine therapy, patients with PIK3CA alterations, including the H1047R mutation, were found at a significantly higher percentage in end-of-treatment samples as compared to pre-treatment samples, suggesting that this mutation may play a role in resistance to fulvestrant (PMID: 30206110). Preclinical studies with mice expressing PIK3CA H1047R demonstrated sensitivity to treatment with RLY-2608 as measured by reduced tumor volume following treatment (Abstract: Varkaris et al. Abstract# CT017, AACR 2023.). JAX-CKB: PIK3CA H1047R is a hotspot mutation that lies within the kinase domain of the Pik3ca protein (UniProt.org). H1047R results in increased phosphorylation of Akt and Mek1/2 and colony formation in culture (PMID: 26627007), and transformation in cell culture (PMID: 29533785, PMID: 17376864).

Database Previews
OncoKB
OncoKB Preview
JAX-CKB
JAX-CKB Preview

Click on previews to view full database entries. External databases may require institutional access.

Computational Analysis

Pathogenicity Predictions

SpliceAI
Predictor Consensus
Mixed/VUS
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied

SpliceAI Scores

Window: ±500bp
Effect Type Score Position
- Acceptor Loss (AL) 0.0 474 bp
- Donor Loss (DL) 0.0 489 bp
+ Acceptor Gain (AG) 0.04 -203 bp
+ Donor Gain (DG) 0.0 491 bp
High impact (≥0.5) Medium impact (0.2-0.49) Low impact (<0.2)

VCEP Guidelines

Applied ACMG/AMP Criteria (VCEP Specific)

Filter Criteria:
PS3

PS3 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PM2

PM2 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PP5

PP5 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

BP4

BP4 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)