PRG4 p.Ile252=
c.756C>T · rs79706370 · VCV3046155
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.07%, afr)
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 -2.9 | GERP -1.4 |
| Overall | ||
| CADD | 0.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.07%
African / African-American · 802/74,974 alleles
Filtering AF
1.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.984%
Overall
0.0541%
873/1,613,726 alleles · low-frequency
exomes 410/1,461,560 · genomes 463/152,166 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.07% | 93 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,785 |
| Admixed American | 0.0433% | 2,308 |
| Middle Eastern | 0.033% | 3,029 |
| South Asian | 0.00769% | 13,011 |
| European (non-Finnish) | 8.48e-05% | 1,179,793 |
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
- PRG4
- Protein
- p.Ile252=
- Coding
- c.756C>T
- MANE Select
- NM_005807
- dbSNP
- rs79706370
- Type
- single nucleotide variant
- Location
- chr1:186306475 (GRCh38)
- Gene constraint
- LOEUF 0.801 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 48.76
- Residue 252
- the 'disordered' region
Similar variants
- PRG4 p.Arg1166Ter Pathogenic/Likely pathogenic ★★ same type
- PRG4 p.Ser1355Ter Pathogenic/Likely pathogenic ★★ same type
- PRG4 p.Ala1246Val Uncertain significance ★★ ⚠ same type
- PRG4 p.Asp87Asn Uncertain significance ★★ ⚠ same type
- PRG4 p.Lys287Arg Uncertain significance ★★ ⚠ same type
- PRG4 p.Pro409Leu Uncertain significance ★★ ⚠ same type
- PRG4 p.Val1399Phe Uncertain significance ★★ ⚠ same type
- PRG4 c.-30-30T>A Benign ★★ 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/prg4-p-ile252 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown