PRMT7 p.Ile292=
c.876C>A · rs2544841251 · VCV3040374
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
PRMT7-related disorder
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 4.1 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 12.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,048 alleles
Overall
6.2e-05%
1/1,614,144 alleles · very rare
exomes 1/1,461,852 · genomes 0/152,292 · joint denominator
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.Ile292=
- Coding
- c.876C>A
- MANE Select
- NM_019023
- dbSNP
- rs2544841251
- Type
- single nucleotide variant
- Location
- chr16:68339917 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 292
- the sam-dependent mtase prmt-type 1 domain
Disease context
PRMT7-related disorder
Similar variants
- PRMT7 c.1056-1G>T Pathogenic/Likely pathogenic ★★ same condition
- PRMT7 p.Arg274Ter Pathogenic/Likely pathogenic ★★ same condition
- PRMT7 c.1324-1G>C Likely pathogenic ★ same condition
- PRMT7 p.Trp17Ter Likely pathogenic ★ same condition
- PRMT7 p.Arg311Gly Uncertain significance ★ ⚠ same condition
- PRMT7 p.Ser79Leu Uncertain significance ★ ⚠ same condition
- PRMT7 p.Leu475fs Likely pathogenic ★ same condition
- PRMT7 p.Leu78fs Likely pathogenic ★ 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-ile292 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown