PRMT7 p.Ile210=
c.630C>T · rs201449196 · VCV3218955
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0466%, afr)
Conditions
1
Inborn genetic diseases
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 -5.2 |
| Overall | ||
| CADD | 8.464 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0466%
African / African-American · 35/75,038 alleles
Filtering AF
0.0345%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0302%
Overall
0.00403%
65/1,614,206 alleles · ultra-rare
exomes 44/1,461,894 · genomes 21/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0466% | 2,144 |
| Admixed American | 0.0167% | 6,002 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,836 |
| European (non-Finnish) | 0.00136% | 73,753 |
| South Asian | 0.0011% | 91,086 |
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.Ile210=
- Coding
- c.630C>T
- MANE Select
- NM_019023
- dbSNP
- rs201449196
- Type
- single nucleotide variant
- Location
- chr16:68339447 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 210
- the sam-dependent mtase prmt-type 1 domain
Similar variants
- PRMT7 p.Glu108Ter Pathogenic/Likely pathogenic ★★ same condition
- PRMT7 p.Ala162Thr Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Ala332Thr Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Ala519Thr Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Ala561Gly Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Arg177Gly Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Arg266Trp Uncertain significance ★★ ⚠ same condition
- PRMT7 p.Arg311Trp Uncertain significance ★★ ⚠ 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-ile210 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown