PDYN p.Ser46=
c.138C>T · rs746996074 · VCV734141
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
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 2.9 | GERP 0.4, phastCons 1 |
| Overall | ||
| CADD | 8.283 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/59,988 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.000558%
9/1,613,842 alleles · ultra-rare
exomes 8/1,461,700 · genomes 1/152,142 · 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
- PDYN
- Protein
- p.Ser46=
- Coding
- c.138C>T
- MANE Select
- NM_024411
- dbSNP
- rs746996074
- Type
- single nucleotide variant
- Location
- chr20:1980950 (GRCh38)
- Gene constraint
- LOEUF 0.769 · pLI 0.49 (gnomAD)
- Structure
- AlphaFold pLDDT 58.95 · 8 PDB
Similar variants
- PDYN p.Ser46Phe 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-ser46 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown