TET3 p.Ser367=
c.1101C>T · rs370396109 · VCV2651036
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.18%, nfe)
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 -1.7 | GERP -5.1 |
| Overall | ||
| CADD | 1.893 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.18%
European (non-Finnish) · 2,119/1,179,880 alleles
Filtering AF
0.173%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.171%
Overall
0.141%
2,281/1,614,020 alleles · rare
exomes 2,162/1,461,704 · genomes 119/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.18% | 557 |
| Remaining individualsnot grpmax-eligible | 0.179% | 558 |
| Admixed American | 0.05% | 2,001 |
| African / African-American | 0.0187% | 5,361 |
| Finnishnot grpmax-eligible | 0.00469% | 21,342 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| South Asian | 0.0022% | 45,543 |
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.Ser367=
- Coding
- c.1101C>T
- MANE Select
- NM_001287491
- dbSNP
- rs370396109
- Type
- single nucleotide variant
- Location
- chr2:74047018 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 52.49 · 2 PDB
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-ser367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown