ILDR1 p.Pro4=
c.12C>G · rs369400454 · VCV2893098
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0056%, 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 -1.1 | GERP -9.3 |
| Overall | ||
| CADD | 2.597 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0056%
European (non-Finnish) · 66/1,178,194 alleles
Filtering AF
0.00452%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00412%
Overall
0.00416%
67/1,609,806 alleles · very rare
exomes 55/1,457,548 · genomes 12/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0056% | 17,851 |
| Admixed American | 0.00168% | 59,634 |
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
- ILDR1
- Protein
- p.Pro4=
- Coding
- c.12C>G
- MANE Select
- NM_001199799
- dbSNP
- rs369400454
- Type
- single nucleotide variant
- Location
- chr3:122022066 (GRCh38)
- Gene constraint
- LOEUF 1.103 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.87
Similar variants
- ILDR1 p.Arg259Ter Pathogenic/Likely pathogenic ★★ same type
- ILDR1 p.Arg462Ter Pathogenic/Likely pathogenic ★★ same type
- ILDR1 p.Cys314Ter Pathogenic/Likely pathogenic ★★ same type
- ILDR1 p.Gln195Ter Pathogenic/Likely pathogenic ★★ same type
- ILDR1 p.Gln274Ter Pathogenic ★★ same type
- ILDR1 p.Gly141Arg Pathogenic/Likely pathogenic ★★ same type
- ILDR1 c.-4C>T Uncertain significance ★★ same type
- ILDR1 p.Ala178Pro 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/ildr1-p-pro4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown