ILDR1 p.Pro255=
c.765G>A · rs571297103 · VCV2969343
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
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 -0.37 | GERP -3.4, phastCons 0.13 |
| Overall | ||
| CADD | 7.789 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,990 alleles
Filtering AF
0.00539%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00389%
Overall
0.0028%
43/1,536,112 alleles · ultra-rare
exomes 32/1,383,802 · genomes 11/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,990 |
| Admixed American | 0.0118% | 8,501 |
| African / African-American | 0.0109% | 9,145 |
| East Asian | 0.00733% | 13,638 |
| Remaining individualsnot grpmax-eligible | 0.00333% | 30,009 |
| South Asian | 0.00238% | 42,028 |
| European (non-Finnish) | 0.00183% | 54,613 |
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.Pro255=
- Coding
- c.765G>A
- MANE Select
- NM_001199799
- dbSNP
- rs571297103
- Type
- single nucleotide variant
- Location
- chr3:121994195 (GRCh38)
- Gene constraint
- LOEUF 1.103 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.87
- Residue 255
- a UniProt-annotated variant site (in dfnb42; loss of interaction with marveld2; loss of tight junction location)
Similar variants
- ILDR1 p.Pro255Ser Uncertain significance ★★ ⚠ same residue
- ILDR1 p.Pro255Leu Benign/Likely benign ★★ same residue
- 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
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-pro255 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown