PSD p.Pro160=
c.480C>T · rs141025645 · VCV730323
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.552%, afr)
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 -0.67 | GERP -3.2, phastCons 0.03 |
| Overall | ||
| CADD | 10.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.552%
African / African-American · 413/74,868 alleles
Filtering AF
0.508%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.49%
Overall
0.0331%
531/1,604,708 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.552% | 181 |
| Middle Eastern | 0.0999% | 1,001 |
| Admixed American | 0.0915% | 1,093 |
| Remaining individualsnot grpmax-eligible | 0.0387% | 2,586 |
| East Asian | 0.00446% | 22,405 |
| European (non-Finnish) | 0.00255% | 39,182 |
| South Asian | 0.00223% | 44,908 |
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.Pro160=
- Coding
- c.480C>T
- MANE Select
- NM_002779
- dbSNP
- rs141025645
- Type
- single nucleotide variant
- Location
- chr10:102416559 (GRCh38)
- Gene constraint
- LOEUF 0.504 · pLI 0.92 (gnomAD)
- Structure
- AlphaFold pLDDT 56.76
- Residue 160
- the 'disordered' region
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-pro160 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown