PDYN p.Ser24=
c.72G>A · rs745951521 · VCV805115
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0494%, sas)
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 0.6 | GERP -4.4, phastCons 0.25 |
| Overall | ||
| CADD | 4.87 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0494%
South Asian · 45/91,082 alleles
Filtering AF
0.0379%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0339%
Overall
0.00651%
105/1,613,944 alleles · ultra-rare
exomes 101/1,461,780 · genomes 4/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0494% | 2,024 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| European (non-Finnish) | 0.00466% | 21,454 |
| African / African-American | 0.00267% | 37,455 |
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
- PDYN
- Protein
- p.Ser24=
- Coding
- c.72G>A
- MANE Select
- NM_024411
- dbSNP
- rs745951521
- Type
- single nucleotide variant
- Location
- chr20:1983013 (GRCh38)
- Gene constraint
- LOEUF 0.769 · pLI 0.49 (gnomAD)
- Structure
- AlphaFold pLDDT 58.95 · 8 PDB
Similar variants
- PDYN p.Ser24Leu Uncertain significance ★★ ⚠ same residue
- PDYN p.Ala190Ser Uncertain significance ★★ ⚠ same type
- PDYN p.Ala20Val Uncertain significance ★★ ⚠ same type
- PDYN p.Arg180Cys Uncertain significance ★★ ⚠ same type
- PDYN p.Arg180Ser Uncertain significance ★★ ⚠ same type
- PDYN p.Arg231Trp Uncertain significance ★★ ⚠ same type
- PDYN p.Cys45Trp Uncertain significance ★★ ⚠ same type
- PDYN p.Glu107Asp 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/pdyn-p-ser24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown