TLR2 p.Phe707=
c.2121T>C · rs5743705 · VCV3037327
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 5.12%, amr) — too common for a highly-penetrant pathogenic allele
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 -6.6 | GERP -4.5 |
| Overall | ||
| CADD | 1.347 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.12%
Admixed American · 3,071/60,020 alleles
Filtering AF
4.97%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.9%
Overall
0.389%
6,285/1,614,082 alleles · common
exomes 5,399/1,461,776 · genomes 886/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 5.12% | 20 |
| East Asian | 4.78% | 21 |
| Remaining individualsnot grpmax-eligible | 0.426% | 235 |
| African / African-American | 0.187% | 536 |
| South Asian | 0.176% | 569 |
| Ashkenazi Jewishnot grpmax-eligible | 0.122% | 822 |
| Middle Eastern | 0.067% | 1,492 |
| Finnishnot grpmax-eligible | 0.0422% | 2,372 |
| European (non-Finnish) | 0.0369% | 2,706 |
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.Phe707=
- Coding
- c.2121T>C
- MANE Select
- NM_001318789
- dbSNP
- rs5743705
- Type
- single nucleotide variant
- Location
- chr4:153705028 (GRCh38)
- Gene constraint
- LOEUF 1.432 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.87 · 7 PDB
- Residue 707
- the tir domain
Disease context
TLR2-related disorder
Similar variants
- TLR2 p.Ala26Val Likely benign same condition
- TLR2 p.Ala400= Benign same condition
- TLR2 p.Asn729Ser Benign same condition
- TLR2 p.Leu563= Benign same condition
- TLR2 p.Leu81Pro Likely 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-phe707 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown