Genetic Information
Gene & Transcript Details
Gene
TET2
Transcript
NM_001127208.2
MANE Select
Total Exons
—
Reference Sequence
NC_000004.11
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_001127208.3 | MANE Select | 9589 nt | 297–6305 |
| NM_001127208.1 | Alternative | 9677 nt | 387–6395 |
| NM_001127208.2 | RefSeq Select | 9796 nt | 488–6496 |
Variant Details
HGVS Notation
NM_001127208.2:c.1379C>T
Protein Change
S460F
Location
Exon 3
(Exon 3 of )
3
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—
Clinical & Population Data
Population Frequency
gnomAD Global Frequency
0.0131 in 100,000
Extremely Rare
ACMG Criteria Applied
PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).
ClinVar
OpenClassification
Uncertain Significance (VUS)
1 publications
Clinical Statement
"This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratories)."
COSMIC Somatic Evidence
OpenCOSMIC ID
COSM53247
Recurrence
4 occurrences
PM1 Criteria
Not Applied
COSMIC Database 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 TET2.
Functional Summary
Error in OpenAI Consolidation. OncoKB: TET2S460FTET2S460FSomaticNCBI Gene:54790|Show additional gene information Variant OverviewTET2, a tumor suppressor and DNA demethylase, is frequently mutated in hematologic malignancies.The TET2 S460F 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
JAX-CKB
Click on previews to view full database entries. External databases may require institutional access.
Computational Analysis
Pathogenicity Predictions
SpliceAIPredictor Consensus
Mixed/VUS
PP3 Applied
No
REVEL Score
0.099
Threshold: ≥0.75 = PP3 applied
SpliceAI Scores
Window: ±500bp| Effect Type | Score | Position |
|---|---|---|
| Acceptor Loss (AL) | 0.0 | None bp |
| Donor Loss (DL) | 0.0 | None bp |
| Acceptor Gain (AG) | 0.0 | None bp |
| Donor Gain (DG) | 0.0 | None 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)