PALLD p.Pro79Ser
c.235C>T · rs2531429599 · VCV2563419
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.055 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.55 | GERP -0.26 |
| Regional constraint | o/e 0.99 | unconstrained · MANE · 387 kb · p 0.73 · regional, not allelic |
| Overall | ||
| CADD | 12.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,180,012 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,614,174 alleles · very rare
exomes 3/1,461,848 · genomes 0/152,326 · 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
- PALLD
- Protein
- p.Pro79Ser
- Coding
- c.235C>T
- MANE Select
- NM_001166108
- dbSNP
- rs2531429599
- Type
- single nucleotide variant
- Location
- chr4:168511739 (GRCh38)
- Gene constraint
- LOEUF 0.644 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.74 · 2 PDB
- Residue 79
- the 'disordered' region
Similar variants
- PALLD p.Pro79Arg Uncertain significance ★ same residue
- PALLD p.Pro79= Likely benign ★ 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
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-pro79ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown