PALLD p.Pro402Ser
c.1204C>T · rs1781708008 · VCV3226717
Uncertain significance
Single submitter
Classification
Uncertain significance
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. | ||
| REVEL | 0.408 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.4, phastCons 1 |
| Regional constraint | o/e 0.99 | unconstrained · MANE · 387 kb · p 0.73 · regional, not allelic |
| Overall | ||
| CADD | 24.0 | 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
- PALLD
- Protein
- p.Pro402Ser
- Coding
- c.1204C>T
- MANE Select
- NM_001166108
- dbSNP
- rs1781708008
- Type
- single nucleotide variant
- Location
- chr4:168683047 (GRCh38)
- Gene constraint
- LOEUF 0.644 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.74 · 2 PDB
Similar variants
- PALLD p.Pro402Ala Uncertain significance ★★ same residue
- PALLD c.1965-12532C>A Uncertain significance ★★ same type
- PALLD c.1965-12532C>G Uncertain significance ★★ same type
- PALLD c.1965-12534C>A Uncertain significance ★★ same type
- PALLD c.1965-12535A>C Uncertain significance ★★ same type
- PALLD c.1965-12544A>G Uncertain significance ★★ same type
- PALLD c.1965-12549T>C Uncertain significance ★★ same type
- PALLD c.1965-12552G>C 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/palld-p-pro402ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown