WDR62 p.Ser992=
c.2976G>A · rs757294519 · VCV195862
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 10 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0932%, nfe)
Conditions
1
microcephaly 2, primary, autosomal recessive, with or without cortical malformations
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 -4.3 |
| Overall | ||
| CADD | 0.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0932%
European (non-Finnish) · 1,068/1,146,184 alleles
Filtering AF
0.0885%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0866%
Overall
0.0766%
1,187/1,550,092 alleles · ultra-rare
exomes 1,109/1,397,806 · genomes 78/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0932% | 1,073 |
| Admixed American | 0.0686% | 1,457 |
| Remaining individualsnot grpmax-eligible | 0.0616% | 1,624 |
| Middle Eastern | 0.0506% | 1,977 |
| South Asian | 0.0345% | 2,898 |
| African / African-American | 0.0109% | 9,141 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00698% | 14,320 |
| Finnishnot grpmax-eligible | 0.00506% | 19,760 |
| East Asian | 0.00489% | 20,451 |
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.Ser992=
- Coding
- c.2976G>A
- MANE Select
- NM_001083961
- dbSNP
- rs757294519
- Type
- single nucleotide variant
- Location
- chr19:36101668 (GRCh38)
- Gene constraint
- LOEUF 0.806 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 61.19
- Residue 992
- the 'disordered' region
Similar variants
- WDR62 p.Ser992Leu Benign/Likely benign ★★ same residue
- WDR62 c.1234-1G>A Pathogenic/Likely pathogenic ★★ same condition
- WDR62 c.269+1G>T Likely pathogenic ★★ same condition
- WDR62 c.3462+1G>A Pathogenic/Likely pathogenic ★★ same condition
- WDR62 c.3462+1G>C Pathogenic/Likely pathogenic ★★ same condition
- WDR62 c.3514+1G>A Pathogenic/Likely pathogenic ★★ same condition
- WDR62 p.Arg438His Pathogenic/Likely pathogenic ★★ same condition
- WDR62 p.Arg512Ter Pathogenic/Likely pathogenic ★★ same condition
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-ser992 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown