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.1173A>G
Protein Change
I391M
Location
Exon 7 (Exon 7 of )
7
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
6.57 in 100,000
Extremely Rare
ACMG Criteria Applied BA1

ClinVar

Open
Classification
Benign
1 publications
Clinical Statement

"This variant has been reported in ClinVar as Benign (7 clinical laboratories) and as Benign by ClinGen Brain Malformations Variant Curation Expert Panel expert panel."

COSMIC Somatic Evidence

Open
COSMIC ID
COSM328028
Recurrence
104 occurrences
PM1 Criteria
Applied
COSMIC Database Preview
COSMIC Preview
Accessing full COSMIC database details requires institutional login or subscription.

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: PIK3CAI391MPIK3CAI391MSomaticNCBI 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.There is conflicting and/or weak data describing the biological significance of the PIK3CA I391M mutation.Hide mutation effect description The PIK3CA I391M mutation is located in the C2 domain in exon 7 of the protein. There is conflicting functional data for this mutation. In vitro kinase assays demonstrated that this mutation is likely neutral as measured by kinase activity comparable to wildtype PIK3CA (PMID: 20530683). However, expression of this mutation in MCF10A but not Ba/F3 cell lines led to proliferation in the absence of growth factors (PMID: 29533785). JAX-CKB: PIK3CA I391M lies within the C2 PI3K-type domain of the Pik3ca protein (UniProt.org). I391M demonstrates kinase activity similar to wild-type Pik3ca in one study (PMID: 20530683), but results in increased cell proliferation and cell viability as compared to wild-type Pik3ca in one of two different cell lines (PMID: 29533785), and therefore, its effect on Pik3ca protein function is unknown.

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 -31 bp
- Donor Loss (DL) 0.0 78 bp
+ Acceptor Gain (AG) 0.0 59 bp
+ Donor Gain (DG) 0.0 -1 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:
BP4

BP4 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

BP6

BP6 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)