TET3 p.Arg147=
c.439C>A · rs182958671 · VCV2651034
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0617%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.26 | GERP -5.1, phastCons 0.66 |
| Overall | ||
| CADD | 5.229 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0617%
Admixed American · 28/45,372 alleles
Filtering AF
0.0438%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0378%
Overall
0.00667%
102/1,529,192 alleles · ultra-rare
exomes 76/1,376,858 · genomes 26/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0617% | 1,620 |
| Remaining individualsnot grpmax-eligible | 0.0187% | 5,342 |
| African / African-American | 0.00555% | 18,022 |
| European (non-Finnish) | 0.00508% | 19,692 |
| East Asian | 0.00226% | 44,342 |
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
- TET3
- Protein
- p.Arg147=
- Coding
- c.439C>A
- MANE Select
- NM_001287491
- dbSNP
- rs182958671
- Type
- single nucleotide variant
- Location
- chr2:74046356 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 52.49 · 2 PDB
- Residue 147
- the 'disordered' region
Similar variants
- TET3 p.Arg1034Ter Pathogenic/Likely pathogenic ★★ same type
- TET3 p.Arg1150Ter Pathogenic ★★ same type
- TET3 p.Arg911Gln Likely pathogenic ★★ same type
- TET3 p.Arg1054His Uncertain significance ★★ ⚠ same type
- TET3 p.Arg1688Cys Uncertain significance ★★ ⚠ same type
- TET3 p.Arg1744His Uncertain significance ★★ ⚠ same type
- TET3 p.Arg430Gly Uncertain significance ★★ ⚠ same type
- TET3 p.Arg604Gln 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/tet3-p-arg147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown