PCDH12 p.Pro155=
c.465C>T · rs958559595 · VCV1580598
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 7.214 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PCDH12
- Protein
- p.Pro155=
- Coding
- c.465C>T
- MANE Select
- NM_016580
- dbSNP
- rs958559595
- Type
- single nucleotide variant
- Location
- chr5:141957387 (GRCh38)
- Gene constraint
- LOEUF 0.752 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.22
- Residue 155
- the cadherin 2 domain
Similar variants
- PCDH12 p.Pro155Leu Uncertain significance ★ ⚠ same residue
- PCDH12 p.Arg151Ter Pathogenic ★★ same type
- PCDH12 p.Arg308Ter Pathogenic/Likely pathogenic ★★ same type
- PCDH12 p.Arg839Ter Pathogenic ★★ same type
- PCDH12 p.Ala1132Thr Uncertain significance ★★ ⚠ same type
- PCDH12 p.Ala148Thr Uncertain significance ★★ ⚠ same type
- PCDH12 p.Ala802Val Uncertain significance ★★ ⚠ same type
- PCDH12 p.Ala905Thr 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/pcdh12-p-pro155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown