IL17RD p.Ser656=
c.1968G>T · rs551495269 · VCV3043465
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00897%, sas)
Conditions
1
IL17RD-related disorder
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 -13 | GERP -5.1 |
| Overall | ||
| CADD | 0.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00897%
South Asian · 8/89,206 alleles
Filtering AF
0.00445%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00318%
Overall
0.000562%
9/1,602,032 alleles · very rare
exomes 7/1,449,748 · genomes 2/152,284 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00897% | 11,151 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,850 |
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.Ser656=
- Coding
- c.1968G>T
- MANE Select
- NM_017563
- dbSNP
- rs551495269
- Type
- single nucleotide variant
- Location
- chr3:57097735 (GRCh38)
- Gene constraint
- LOEUF 0.952 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.68
- Residue 656
- the 'disordered' region
Disease context
IL17RD-related disorder
Similar variants
- IL17RD p.Arg183Gln Uncertain significance ⚠ same condition
- IL17RD p.Gln629Arg Uncertain significance ⚠ same condition
- IL17RD p.Ser257Gly Uncertain significance ⚠ same condition
- IL17RD p.Asp186= Likely benign same condition
- IL17RD p.Cys602= Likely benign same condition
- IL17RD p.His516= Likely benign same condition
- IL17RD p.Leu53= Likely benign same condition
- IL17RD p.Ser662= 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/il17rd-p-ser656 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown