Genetic Information

Gene & Transcript Details

Gene
PTEN
Transcript
NM_000314.8 MANE Select
Total Exons
—
Reference Sequence
NC_000010.10
Alternative Transcripts
IDStatusDetails
NM_000314.7 RefSeq Select 8514 nt | 845–2056
NM_000314.5 Alternative 8719 nt | 1032–2243
NM_000314.4 Alternative 5572 nt | 1032–2243
NM_000314.3 Alternative 3416 nt | 1032–2243
NM_000314.6 Alternative 8718 nt | 1032–2243
NM_000314.8 MANE Select 8515 nt | 846–2057

Variant Details

HGVS Notation
NM_000314.8:c.263A>G
Protein Change
Y88C
Location
Exon 5 (Exon 5 of )
5
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.0 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
Unknown
0 publications
Clinical Statement

""

COSMIC Somatic Evidence

Open
COSMIC ID
COSM5139
Recurrence
11 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 PTEN.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: PTENY88CPTENY88CSomaticNCBI Gene:5728|Show additional gene information Variant OverviewPTEN, a lipid and protein phosphatase, is one of the most frequently mutated genes in cancer.The PTEN Y88C mutation has not specifically been reviewed by the OncoKB team, and therefore its biological significance is unknown. JAX-CKB: PTEN Y88C lies within the phosphatase tensin-type domain of the Pten protein (UniProt.org). Y88C results in lipid phosphatase activity similar to wild-type Pten in yeast (PMID: 21828076), and therefore, is predicted to have no effect on Pten protein function.

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) 0.03 -27 bp
- Donor Loss (DL) 0.0 229 bp
+ Acceptor Gain (AG) 0.0 99 bp
+ Donor Gain (DG) 0.0 107 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)

PM2

PM2 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PS3

PS3 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)