WAC p.Pro314=
c.942C>T · rs753031346 · VCV750972
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.011%, sas)
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 0.18 | GERP -3.9, phastCons 0.96 |
| Overall | ||
| CADD | 6.587 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.011%
South Asian · 10/91,076 alleles
Filtering AF
0.00594%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00453%
Overall
0.00118%
19/1,613,968 alleles · ultra-rare
exomes 17/1,461,836 · genomes 2/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.011% | 9,108 |
| Admixed American | 0.00167% | 59,994 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| African / African-American | 0.00134% | 74,902 |
| European (non-Finnish) | 0.000508% | 196,674 |
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
- WAC
- Protein
- p.Pro314=
- Coding
- c.942C>T
- MANE Select
- NM_016628
- dbSNP
- rs753031346
- Type
- single nucleotide variant
- Location
- chr10:28608208 (GRCh38)
- Gene constraint
- LOEUF 0.248 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.71
- Residue 314
- the 'disordered' region; a UniProt-annotated variant site (found in a patient with severe intellectual disability; likely pathogenic)
Similar variants
- WAC p.Pro314His Uncertain significance ★ ⚠ same residue
- WAC c.1437+1G>A Pathogenic/Likely pathogenic ★★ same type
- WAC c.1746+2T>C Pathogenic ★★ same type
- WAC c.381+1G>T Likely pathogenic ★★ same type
- WAC p.Arg151Ter Pathogenic ★★ same type
- WAC p.Arg47Ter Pathogenic ★★ same type
- WAC p.Arg513Ter Pathogenic ★★ same type
- WAC p.Arg550Ter 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/wac-p-pro314 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown