IL17RD p.Pro557=
c.1671C>G · rs144425478 · VCV760875
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00195%, nfe)
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 -4.4 | GERP -4.8 |
| Overall | ||
| CADD | 0.394 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00195%
European (non-Finnish) · 23/1,179,900 alleles
Filtering AF
0.0013%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00108%
Overall
0.00149%
24/1,613,870 alleles · very rare
exomes 21/1,461,704 · genomes 3/152,166 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00195% | 51,300 |
| African / African-American | 0.00133% | 74,914 |
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
- IL17RD
- Protein
- p.Pro557=
- Coding
- c.1671C>G
- MANE Select
- NM_017563
- dbSNP
- rs144425478
- Type
- single nucleotide variant
- Location
- chr3:57098032 (GRCh38)
- Gene constraint
- LOEUF 0.952 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.68
Similar variants
- IL17RD p.Pro557Ser Uncertain significance ★ same residue
- IL17RD c.814-3C>T Uncertain significance ★★ same type
- IL17RD p.Ala458Gly Uncertain significance ★★ ⚠ same type
- IL17RD p.Arg203Gln Uncertain significance ★★ ⚠ same type
- IL17RD p.Arg355Gln Uncertain significance ★★ ⚠ same type
- IL17RD p.Asn19Ser Uncertain significance ★★ ⚠ same type
- IL17RD p.Gln523His Uncertain significance ★★ ⚠ same type
- IL17RD p.Gln563Arg 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/il17rd-p-pro557 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown