PRMT1 p.Thr327=
c.981G>A · rs149767260 · VCV2650283
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0709%, mid)
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 -11 | |
| Overall | ||
| CADD | 1.342 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0709%
Middle Eastern · 4/5,638 alleles
Filtering AF
0.0242%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0146%
Overall
0.0062%
100/1,612,630 alleles · ultra-rare
exomes 92/1,460,894 · genomes 8/151,736 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0709% | 1,410 |
| European (non-Finnish) | 0.00721% | 13,878 |
| South Asian | 0.00549% | 18,207 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,798 |
| African / African-American | 0.00402% | 24,901 |
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
- PRMT1
- Protein
- p.Thr327=
- Coding
- c.981G>A
- MANE Select
- NM_001536
- dbSNP
- rs149767260
- Type
- single nucleotide variant
- Location
- chr19:49686675 (GRCh38)
- Gene constraint
- LOEUF 0.218 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.14 · 8 PDB
- Residue 327
- the sam-dependent mtase prmt-type domain
Similar variants
- PRMT1 p.Thr327Met Uncertain significance ★ ⚠ same residue
- PRMT1 p.Glu45= Benign ★★ same type
- PRMT1 p.Ala249Thr Uncertain significance ★ ⚠ same type
- PRMT1 p.Ala44Pro Uncertain significance ★ ⚠ same type
- PRMT1 p.Ala7Val Uncertain significance ★ ⚠ same type
- PRMT1 p.Arg112His Uncertain significance ★ ⚠ same type
- PRMT1 p.Arg195Gln Uncertain significance ★ same type
- PRMT1 p.Arg206Gln 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/prmt1-p-thr327 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown