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.2015+9A>G
Protein Change
?
Location
Exon 13 (Exon 13 of )
13
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.0124 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 Benign
2 publications
Clinical Statement

"This variant has been reported in ClinVar as Likely benign (1 clinical laboratories) and as Benign (1 clinical laboratories) and as Likely benign by ClinGen Brain Malformations Variant Curation Expert Panel expert panel."

COSMIC Somatic Evidence

Open
COSMIC ID
Recurrence
0 occurrences
PM1 Criteria
Not 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: PIK3CA2015+9A>GPIK3CA2015+9A>GSomaticNCBI 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 2015+9a>G mutation has not specifically been reviewed by the OncoKB team, and therefore its biological significance is unknown. JAX-CKB: No results found

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 -161 bp
- Donor Loss (DL) 0.0 -77 bp
+ Acceptor Gain (AG) 0.0 -112 bp
+ Donor Gain (DG) 0.0 25 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:
PM2

PM2 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

BP4

BP4 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

BP6

BP6 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)