PRMT7 p.Thr498=
c.1494C>T · rs61742685 · VCV1461639
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0158%, nfe)
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 -4.3 | GERP -5.2 |
| Overall | ||
| CADD | 1.393 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0158%
European (non-Finnish) · 186/1,180,020 alleles
Filtering AF
0.0138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0132%
Overall
0.0123%
198/1,612,750 alleles · ultra-rare
exomes 190/1,460,544 · genomes 8/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0158% | 6,344 |
| African / African-American | 0.00801% | 12,488 |
| East Asian | 0.00668% | 14,961 |
| Admixed American | 0.00167% | 60,000 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
| South Asian | 0.0011% | 91,088 |
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.Thr498=
- Coding
- c.1494C>T
- MANE Select
- NM_019023
- dbSNP
- rs61742685
- Type
- single nucleotide variant
- Location
- chr16:68352328 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 498
- the sam-dependent mtase prmt-type 2 domain
Similar variants
- 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
- PRMT7 p.Ala162Thr 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/prmt7-p-thr498 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown