TBL2 p.Pro334=
c.1002G>A · rs782702563 · VCV732510
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0233%, 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 -13 | GERP -3.7 |
| Overall | ||
| CADD | 0.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0233%
Admixed American · 14/60,032 alleles
Filtering AF
0.0141%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0112%
Overall
0.00235%
38/1,613,786 alleles · ultra-rare
exomes 29/1,461,392 · genomes 9/152,394 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0233% | 4,288 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.00533% | 18,770 |
| South Asian | 0.00329% | 30,361 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
| Finnishnot grpmax-eligible | 0.00315% | 31,793 |
| East Asian | 0.00223% | 44,892 |
| European (non-Finnish) | 0.000932% | 107,275 |
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
- TBL2
- Protein
- p.Pro334=
- Coding
- c.1002G>A
- MANE Select
- NM_012453
- dbSNP
- rs782702563
- Type
- single nucleotide variant
- Location
- chr7:73570849 (GRCh38)
- Gene constraint
- LOEUF 1.054 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.11
Similar variants
- TBL2 p.Ala189= Benign/Likely benign ★★ same type
- TBL2 p.Ala332= Benign/Likely benign ★★ same type
- TBL2 p.Gln229= Benign ★★ same type
- TBL2 p.Glu135= Benign ★★ same type
- TBL2 p.Glu257Ala Benign ★★ same type
- TBL2 c.599-7C>A Uncertain significance ★ same type
- TBL2 p.Ala139Thr Uncertain significance ★ ⚠ same type
- TBL2 p.Ala139Val 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/tbl2-p-pro334 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown