WHRN p.Val620=
c.1860C>T · rs545711776 · VCV1116144
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 3.3 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 1.305 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,882 alleles
Overall
6.2e-05%
1/1,614,170 alleles · very rare
exomes 1/1,461,818 · genomes 0/152,352 · 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
- WHRN
- Protein
- p.Val620=
- Coding
- c.1860C>T
- MANE Select
- NM_015404
- dbSNP
- rs545711776
- Type
- single nucleotide variant
- Location
- chr9:114406731 (GRCh38)
- Gene constraint
- LOEUF 0.808 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 59.39 · 5 PDB
- Residue 620
- the 'disordered' region
Similar variants
- 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
- WHRN p.Ala207Ser Uncertain significance ★★ ⚠ same type
- WHRN p.Ala315Pro 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-val620 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown