TBCE p.Pro402=
c.1206G>A · rs369000163 · VCV1612337
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0283%, 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 -0.98 | GERP -3.7 |
| Overall | ||
| CADD | 7.209 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0283%
Admixed American · 17/60,004 alleles
Filtering AF
0.0187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0157%
Overall
0.00514%
83/1,614,076 alleles · ultra-rare
exomes 55/1,461,894 · genomes 28/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0283% | 3,530 |
| African / African-American | 0.028% | 3,572 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,930 |
| East Asian | 0.00669% | 14,957 |
| European (non-Finnish) | 0.00297% | 33,715 |
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
- TBCE
- Protein
- p.Pro402=
- Coding
- c.1206G>A
- MANE Select
- NM_003193
- dbSNP
- rs369000163
- Type
- single nucleotide variant
- Location
- chr1:235438858 (GRCh38)
- Gene constraint
- LOEUF 0.868 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.27 · 6 PDB
Similar variants
- TBCE p.Pro402Leu Uncertain significance ★ ⚠ same residue
- TBCE c.100+1G>A Pathogenic/Likely pathogenic ★★ same type
- TBCE p.Arg12Ter Likely pathogenic ★★ same type
- TBCE p.Gln123Ter Pathogenic/Likely pathogenic ★★ same type
- TBCE p.Ile155Asn Pathogenic/Likely pathogenic ★★ same type
- TBCE p.Lys145Ter Pathogenic/Likely pathogenic ★★ same type
- B3GALNT2 p.Gly492Ser Uncertain significance ★★ ⚠ same type
- TBCE c.738-3C>T 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/tbce-p-pro402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown