PSD p.Ser518=
c.1554C>T · VCV3939371
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0213%, 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 -1 | GERP -4 |
| Overall | ||
| CADD | 4.178 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0213%
African / African-American · 16/74,950 alleles
Filtering AF
0.0133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0109%
Overall
0.00361%
58/1,608,608 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0213% | 4,684 |
| European (non-Finnish) | 0.00323% | 30,966 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,116 |
| Finnishnot grpmax-eligible | 0.00158% | 63,182 |
| South Asian | 0.0011% | 90,716 |
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.Ser518=
- Coding
- c.1554C>T
- MANE Select
- NM_002779
- Type
- single nucleotide variant
- Location
- chr10:102412575 (GRCh38)
- Gene constraint
- LOEUF 0.504 · pLI 0.92 (gnomAD)
- Structure
- AlphaFold pLDDT 56.76
- Residue 518
- the sec7 domain; 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-ser518 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown