WDR62 p.Ser1237=
c.3711T>C · rs887740291 · VCV3014998
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00314%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.22 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.2 | GERP -3.4 |
| Overall | ||
| CADD | 0.362 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00314%
European (non-Finnish) · 37/1,180,000 alleles
Filtering AF
0.00231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00202%
Overall
0.00229%
37/1,614,000 alleles · very rare
exomes 37/1,461,768 · genomes 0/152,232 · 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
- WDR62
- Protein
- p.Ser1237=
- Coding
- c.3711T>C
- MANE Select
- NM_001083961
- dbSNP
- rs887740291
- Type
- single nucleotide variant
- Location
- chr19:36103539 (GRCh38)
- Gene constraint
- LOEUF 0.806 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 61.19
Similar variants
- WDR62 p.Ser1237fs Likely pathogenic ★ same residue
- 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
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-ser1237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown