TET2 p.Pro465=
c.1395A>G · rs145700876 · VCV2059422
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.201%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.48 | GERP -3.4 |
| Overall | ||
| CADD | 2.193 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.201%
African / African-American · 151/75,016 alleles
Filtering AF
0.175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.165%
Overall
0.0103%
167/1,614,072 alleles · rare
exomes 81/1,461,826 · genomes 86/152,246 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.201% | 497 |
| Middle Eastern | 0.0165% | 6,060 |
| Admixed American | 0.0117% | 8,573 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,930 |
| South Asian | 0.0011% | 91,074 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- TET2
- Protein
- p.Pro465=
- Coding
- c.1395A>G
- MANE Select
- NM_001127208
- dbSNP
- rs145700876
- Type
- single nucleotide variant
- Location
- chr4:105235337 (GRCh38)
- Gene constraint
- LOEUF 1.997 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.31 · 6 PDB
- Residue 465
- the 'disordered' region
Similar variants
- TET2 p.Arg544Ter Pathogenic/Likely pathogenic ★★ same type
- TET2 p.Gln622Ter Pathogenic/Likely pathogenic ★★ same type
- TET2 c.3409+42G>T Uncertain significance ★★ same type
- TET2 p.Ala1072Pro Uncertain significance ★★ ⚠ same type
- TET2 p.Ala1158Val Uncertain significance ★★ same type
- TET2 p.Ala1769Pro Uncertain significance ★★ ⚠ same type
- TET2 p.Arg1095Lys Uncertain significance ★★ ⚠ same type
- TET2 p.Arg1134Thr Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/tet2-p-pro465 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown