TET2 p.Pro474=
c.1422G>A · rs774920451 · VCV2907735
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, eas)
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 0.98 | GERP -0.43, phastCons 0.002 |
| Overall | ||
| CADD | 3.602 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,888 alleles
Filtering AF
0.00726%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00514%
Overall
0.00173%
28/1,614,014 alleles · ultra-rare
exomes 22/1,461,848 · genomes 6/152,166 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0156% | 6,413 |
| Admixed American | 0.00167% | 60,000 |
| European (non-Finnish) | 0.00161% | 62,107 |
| African / African-American | 0.00134% | 74,900 |
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.Pro474=
- Coding
- c.1422G>A
- MANE Select
- NM_001127208
- dbSNP
- rs774920451
- Type
- single nucleotide variant
- Location
- chr4:105235364 (GRCh38)
- Gene constraint
- LOEUF 1.997 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.31 · 6 PDB
- Residue 474
- the 'disordered' region
Similar variants
- TET2 p.Pro474Gln Uncertain significance ★ ⚠ same residue
- TET2 p.Pro474Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro474 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown