WHRN p.Pro239=
c.717G>A · rs1437523406 · VCV2878018
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00266%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -4.1 |
| Overall | ||
| CADD | 0.733 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00266%
African / African-American · 2/75,052 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.00136%
22/1,612,986 alleles · very rare
exomes 22/1,460,660 · genomes 0/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00266% | 37,526 |
| Admixed American | 0.00167% | 59,970 |
| European (non-Finnish) | 0.00161% | 62,100 |
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
- WHRN
- Protein
- p.Pro239=
- Coding
- c.717G>A
- MANE Select
- NM_015404
- dbSNP
- rs1437523406
- Type
- single nucleotide variant
- Location
- chr9:114478673 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 59.39 · 5 PDB
Similar variants
- WHRN p.Pro239Leu Uncertain significance ★★ ⚠ same residue
- WHRN p.Pro239Lys Uncertain significance ★ same residue
- WHRN c.1203+2T>C Likely pathogenic ★★ same type
- WHRN c.1417-1G>A Pathogenic/Likely pathogenic ★★ same type
- WHRN p.Arg778Ter Pathogenic ★★ same type
- WHRN p.Gln187Ter Pathogenic/Likely pathogenic ★★ same type
- WHRN p.Trp374Ter Pathogenic/Likely pathogenic ★★ same type
- WHRN c.*156G>A 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/whrn-p-pro239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown