PSD p.Ser10=
c.30G>A · rs200392028 · VCV744259
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0263%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.2 |
| Overall | ||
| CADD | 1.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0263%
Admixed American · 15/57,032 alleles
Filtering AF
0.0161%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0131%
Overall
0.00449%
71/1,582,336 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0263% | 3,802 |
| South Asian | 0.0123% | 8,155 |
| African / African-American | 0.0108% | 9,230 |
| Remaining individualsnot grpmax-eligible | 0.00486% | 20,562 |
| European (non-Finnish) | 0.00281% | 35,539 |
| East Asian | 0.00229% | 43,612 |
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
- PSD
- Protein
- p.Ser10=
- Coding
- c.30G>A
- MANE Select
- NM_002779
- dbSNP
- rs200392028
- Type
- single nucleotide variant
- Location
- chr10:102417009 (GRCh38)
- Gene constraint
- LOEUF 0.504 · pLI 0.92 (gnomAD)
- Structure
- AlphaFold pLDDT 56.76
Similar variants
- PSD p.Gly336Ser Benign ★★ same type
- PSD p.Leu659= Benign ★★ same type
- PSD p.Ala1017Pro Uncertain significance ★ ⚠ same type
- PSD p.Ala185Pro Uncertain significance ★ ⚠ same type
- PSD p.Ala204Val Uncertain significance ★ ⚠ same type
- PSD p.Ala260Val Uncertain significance ★ ⚠ same type
- PSD p.Ala311Asp Uncertain significance ★ ⚠ same type
- PSD p.Ala457Thr 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/psd-p-ser10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown