PSMA4 p.Ser168=
c.504C>T · VCV3426906
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, sas)
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 -8.7 | GERP -5.6 |
| Overall | ||
| CADD | 1.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/90,996 alleles
Filtering AF
0.0101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00812%
Overall
0.00564%
91/1,613,338 alleles · ultra-rare
exomes 84/1,461,238 · genomes 7/152,100 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,066 |
| Middle Eastern | 0.0164% | 6,080 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,939 |
| Admixed American | 0.0134% | 7,485 |
| European (non-Finnish) | 0.00475% | 21,067 |
| East Asian | 0.00446% | 22,437 |
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
- PSMA4
- Protein
- p.Ser168=
- Coding
- c.504C>T
- MANE Select
- NM_002789
- Type
- single nucleotide variant
- Location
- chr15:78545761 (GRCh38)
- Gene constraint
- LOEUF 0.409 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 93.17 · 177 PDB
- Residue 168
- an α-helix
Similar variants
- PSMA4 p.Ser168Asn Uncertain significance ★ ⚠ same residue
- PSMA4 p.Ala113= Benign ★★ same type
- PSMA4 p.Ala169Thr Uncertain significance ★ ⚠ same type
- PSMA4 p.Glu242Lys Uncertain significance ★ ⚠ same type
- PSMA4 p.Ile164Val Uncertain significance ★ ⚠ same type
- PSMA4 p.Ile194Val Uncertain significance ★ ⚠ same type
- PSMA4 p.Ile93Ser Uncertain significance ★ same type
- PSMA4 p.Leu190Pro 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/psma4-p-ser168 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown