PRMT7 p.Ser280=
c.840G>A · rs141861333 · VCV1595886
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0114%, nfe)
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 -0.45 | GERP -3.7, phastCons 0.031 |
| Overall | ||
| CADD | 11.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0114%
European (non-Finnish) · 135/1,180,040 alleles
Filtering AF
0.00986%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0092%
Overall
0.00886%
143/1,614,040 alleles · ultra-rare
exomes 142/1,461,886 · genomes 1/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0114% | 8,741 |
| South Asian | 0.00659% | 15,179 |
| East Asian | 0.00223% | 44,898 |
| Admixed American | 0.00167% | 59,996 |
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.Ser280=
- Coding
- c.840G>A
- MANE Select
- NM_019023
- dbSNP
- rs141861333
- Type
- single nucleotide variant
- Location
- chr16:68339881 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 280
- the sam-dependent mtase prmt-type 1 domain
Similar variants
- PRMT7 p.Ser280Thr Uncertain significance ★ ⚠ 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-ser280 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown