PRMT7 p.Pro588Leu
c.1763C>T · rs370795284 · VCV1986463
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0767 | likely benign |
|---|---|---|
| REVEL | 0.035 | moderately benign-leaning |
| SaProt | LLR -8.97 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.20 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 0.41 | GERP -2.5, phastCons 0.036 |
| Regional constraint | o/e 0.95 | unconstrained · MANE · 41 kb · p 0.12 · regional, not allelic |
| Overall | ||
| CADD | 4.238 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0331% | 3,024 |
| Admixed American | 0.00667% | 14,987 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,606 |
| African / African-American | 0.00267% | 37,507 |
| East Asian | 0.00223% | 44,780 |
| South Asian | 0.0011% | 90,922 |
| European (non-Finnish) | 0.000848% | 117,925 |
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
- PRMT7
- Protein
- p.Pro588Leu
- Coding
- c.1763C>T
- MANE Select
- NM_019023
- dbSNP
- rs370795284
- Type
- single nucleotide variant
- Location
- chr16:68355835 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 588
- the sam-dependent mtase prmt-type 2 domain
Similar variants
- PRMT7 p.Pro588= Likely benign ★★ same residue
- PRMT7 p.Glu108Ter Pathogenic/Likely pathogenic ★★ same condition
- PRMT7 p.Ala162Thr Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Ala332Thr Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Ala519Thr Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Ala561Gly Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Arg177Gly Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Arg266Trp Uncertain significance ★★ ⚠ same condition
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/prmt7-p-pro588leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown