PRMT7 p.Pro588=
c.1764G>A · rs140624242 · VCV1336887
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0973%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.7 | GERP -5.3 |
| Overall | ||
| CADD | 0.418 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0973%
African / African-American · 73/75,010 alleles
Filtering AF
0.0793%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0727%
Overall
0.00596%
96/1,609,428 alleles · ultra-rare
exomes 58/1,457,110 · genomes 38/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0973% | 1,028 |
| Admixed American | 0.0134% | 7,491 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,402 |
| East Asian | 0.00223% | 44,764 |
| Finnishnot grpmax-eligible | 0.00165% | 60,720 |
| South Asian | 0.0011% | 90,898 |
| European (non-Finnish) | 0.000509% | 196,532 |
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.Pro588=
- Coding
- c.1764G>A
- MANE Select
- NM_019023
- dbSNP
- rs140624242
- Type
- single nucleotide variant
- Location
- chr16:68355836 (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.Pro588Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- PRMT7 c.1056-1G>T Pathogenic/Likely pathogenic ★★ same type
- PRMT7 p.Arg274Ter Pathogenic/Likely pathogenic ★★ same type
- PRMT7 p.Arg390Ter Pathogenic ★★ same type
- PRMT7 p.Cys571Ter Pathogenic ★★ same type
- PRMT7 p.Gln323Ter Pathogenic ★★ same type
- PRMT7 p.Glu108Ter Pathogenic/Likely pathogenic ★★ same type
- PRMT7 p.Tyr159Ter Pathogenic ★★ 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/prmt7-p-pro588 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown