ILDR1 p.Pro18=
c.54A>C · rs1421683329 · VCV1993491
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00102%, 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 -0.73 | GERP -4.4 |
| Overall | ||
| CADD | 8.072 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00102%
European (non-Finnish) · 12/1,178,730 alleles
Filtering AF
0.000543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000429%
Overall
0.000745%
12/1,611,082 alleles · very rare
exomes 12/1,458,722 · genomes 0/152,360 · joint denominator
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.Pro18=
- Coding
- c.54A>C
- MANE Select
- NM_001199799
- dbSNP
- rs1421683329
- Type
- single nucleotide variant
- Location
- chr3:122022024 (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-pro18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown