WDR36 p.Val658=
c.1974C>G · rs17624563 · VCV1222170
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 23.4%, sas) — too common for a highly-penetrant pathogenic allele
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 1.3 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 2.835 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
23.4%
South Asian · 21,281/90,972 alleles
Filtering AF
23.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 23%
Overall
10.1%
162,204/1,611,152 alleles · common
exomes 145,779/1,459,066 · genomes 16,425/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 23.4% | 4 |
| African / African-American | 12.3% | 8 |
| Middle Eastern | 11.4% | 9 |
| Finnishnot grpmax-eligible | 10.6% | 9 |
| Remaining individualsnot grpmax-eligible | 10.3% | 10 |
| European (non-Finnish) | 9.32% | 11 |
| Ashkenazi Jewishnot grpmax-eligible | 8.18% | 12 |
| Admixed American | 5.62% | 18 |
| East Asian | 4.89% | 20 |
| Amishnot grpmax-eligible | 4.28% | 23 |
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
- WDR36
- Protein
- p.Val658=
- Coding
- c.1974C>G
- MANE Select
- NM_139281
- dbSNP
- rs17624563
- Type
- single nucleotide variant
- Location
- chr5:111120565 (GRCh38)
- Gene constraint
- LOEUF 0.706 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.47 · 3 PDB
Similar variants
- WDR36 p.Ala297Ser Uncertain significance ★★ same type
- WDR36 p.Ala75Thr Uncertain significance ★★ same type
- WDR36 p.Arg374His Uncertain significance ★★ same type
- WDR36 p.Arg473Gln Uncertain significance ★★ ⚠ same type
- WDR36 p.Asn87Ser Uncertain significance ★★ ⚠ same type
- WDR36 p.Asp571His Uncertain significance ★★ ⚠ same type
- WDR36 p.Asp686Val Uncertain significance ★★ ⚠ same type
- WDR36 p.Glu674Gly 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/wdr36-p-val658 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown