WDR62 p.Pro925=
c.2775C>T · VCV4753507
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, 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 -0.83 | GERP -4.7 |
| Overall | ||
| CADD | 2.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
African / African-American · 10/74,940 alleles
Filtering AF
0.00723%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0055%
Overall
0.000991%
16/1,614,096 alleles · ultra-rare
exomes 8/1,461,848 · genomes 8/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0133% | 7,494 |
| European (non-Finnish) | 0.000508% | 196,672 |
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
- WDR62
- Protein
- p.Pro925=
- Coding
- c.2775C>T
- MANE Select
- NM_001083961
- Type
- single nucleotide variant
- Location
- chr19:36100783 (GRCh38)
- Gene constraint
- LOEUF 0.806 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 61.19
- Residue 925
- the 'disordered' region
Similar variants
- WDR62 c.1234-1G>A Pathogenic/Likely pathogenic ★★ same type
- WDR62 c.177+1G>C Pathogenic/Likely pathogenic ★★ same type
- WDR62 c.2333+2T>C Likely pathogenic ★★ same type
- WDR62 c.2520+5G>T Pathogenic ★★ same type
- WDR62 c.269+1G>T Likely pathogenic ★★ same type
- WDR62 c.3462+1G>A Pathogenic/Likely pathogenic ★★ same type
- WDR62 c.3462+1G>C Pathogenic/Likely pathogenic ★★ same type
- WDR62 c.3514+1G>A 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/wdr62-p-pro925 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown