TLR2 p.Ala400=
c.1200A>G · rs144038898 · VCV3035354
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.428%, eas)
Conditions
1
TLR2-related disorder
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 0.53 | GERP -4.1, phastCons 0.001 |
| Overall | ||
| CADD | 2.543 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.428%
East Asian · 192/44,878 alleles
Filtering AF
0.378%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.359%
Overall
0.0128%
207/1,614,110 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.428% | 234 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| South Asian | 0.00329% | 30,350 |
| European (non-Finnish) | 0.000169% | 590,002 |
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
- TLR2
- Protein
- p.Ala400=
- Coding
- c.1200A>G
- MANE Select
- NM_001318789
- dbSNP
- rs144038898
- Type
- single nucleotide variant
- Location
- chr4:153704107 (GRCh38)
- Gene constraint
- LOEUF 1.432 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.87 · 7 PDB
Disease context
TLR2-related disorder
Similar variants
- TLR2 p.Ala26Val Likely benign same condition
- TLR2 p.Asn729Ser Benign same condition
- TLR2 p.Leu563= Benign same condition
- TLR2 p.Leu81Pro Likely benign same condition
- TLR2 p.Phe707= Benign same condition
- TLR2 p.Pro456= Likely benign same condition
- TLR2 p.Thr411Ile Benign same condition
- TLR2 p.Thr65= Likely benign same condition
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/tlr2-p-ala400 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown