TLR7 p.Pro1016=
c.3048A>C · rs150367536 · VCV2060084
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.199%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.11 | GERP -4.4 |
| Overall | ||
| CADD | 3.728 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.199%
Admixed American · 91/45,672 alleles
Filtering AF
0.166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.154%
Overall
0.0169%
205/1,209,825 alleles · rare
exomes 160/1,098,216 · genomes 45/111,609 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.199% | 502 |
| Middle Eastern | 0.0457% | 2,186 |
| Remaining individualsnot grpmax-eligible | 0.0315% | 3,173 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0136% | 7,347 |
| European (non-Finnish) | 0.00983% | 10,173 |
| African / African-American | 0.00876% | 11,419 |
| South Asian | 0.00176% | 56,801 |
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
- TLR7
- Protein
- p.Pro1016=
- Coding
- c.3048A>C
- MANE Select
- NM_016562
- dbSNP
- rs150367536
- Type
- single nucleotide variant
- Location
- chrX:12888556 (GRCh38)
- Structure
- AlphaFold pLDDT 87.60 · 1 PDB
- Residue 1016
- the tir domain
Similar variants
- TLR7 p.Arg357Cys Uncertain significance ★★ ⚠ same type
- TLR7 p.Asn159Asp Uncertain significance ★★ ⚠ same type
- TLR7 p.Asn720Ser Uncertain significance ★★ ⚠ same type
- TLR7 p.Asp198Gly Uncertain significance ★★ ⚠ same type
- TLR7 p.Asp438Val Uncertain significance ★★ ⚠ same type
- TLR7 p.Cys889Tyr Uncertain significance ★★ ⚠ same type
- TLR7 p.Gln117Lys Uncertain significance ★★ ⚠ same type
- TLR7 p.Gln823Glu 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/tlr7-p-pro1016 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown