PSMD4 p.Val92=
c.276G>C · rs139032841 · VCV771118
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.464%, mid)
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 0.56 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 7.514 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.464%
Middle Eastern · 28/6,028 alleles
Filtering AF
0.417%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.403%
Overall
0.0518%
825/1,591,516 alleles · rare
exomes 754/1,439,256 · genomes 71/152,260 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.464% | 215 |
| South Asian | 0.454% | 220 |
| Amishnot grpmax-eligible | 0.22% | 455 |
| Remaining individualsnot grpmax-eligible | 0.0632% | 1,582 |
| Admixed American | 0.0313% | 3,192 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0309% | 3,240 |
| European (non-Finnish) | 0.0279% | 3,583 |
| African / African-American | 0.00539% | 18,568 |
| East Asian | 0.0023% | 43,468 |
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
- PSMD4
- Protein
- p.Val92=
- Coding
- c.276G>C
- MANE Select
- NM_002810
- dbSNP
- rs139032841
- Type
- single nucleotide variant
- Location
- chr1:151264022 (GRCh38)
- Gene constraint
- LOEUF 0.295 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.72 · 133 PDB
- Residue 92
- the vwfa domain; an α-helix
Similar variants
- PSMD4 p.Thr250= Benign ★★ same type
- PSMD4 p.Ala259Asp Uncertain significance ★ ⚠ same type
- PSMD4 p.Ala259Thr Uncertain significance ★ ⚠ same type
- PSMD4 p.Ala303Val Uncertain significance ★ ⚠ same type
- PSMD4 p.Ala55Ser Uncertain significance ★ ⚠ same type
- PSMD4 p.Arg108His Uncertain significance ★ ⚠ same type
- PSMD4 p.Arg230Trp Uncertain significance ★ ⚠ same type
- PSMD4 p.Arg237Gln 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/psmd4-p-val92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown