TLR7 p.Pro1019=
c.3057G>A · rs985509507 · VCV2788687
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00173%, afr)
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 -0.4 | GERP -4.4 |
| Overall | ||
| CADD | 2.847 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00173%
African / African-American · 1/57,720 alleles
Filtering AF
0.000105%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 7.1e-05%
Overall
0.000413%
5/1,211,426 alleles · very rare
exomes 5/1,098,077 · genomes 0/113,349 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00173% | 57,720 |
| European (non-Finnish) | 0.000447% | 223,841 |
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.Pro1019=
- Coding
- c.3057G>A
- MANE Select
- NM_016562
- dbSNP
- rs985509507
- Type
- single nucleotide variant
- Location
- chrX:12888565 (GRCh38)
- Structure
- AlphaFold pLDDT 87.60 · 1 PDB
- Residue 1019
- the tir domain
Similar variants
- TLR7 p.Pro1019Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro1019 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown