PRMT7 p.His200=
c.600C>T · rs138720818 · VCV777039
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.34%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.50 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -5.2 |
| Overall | ||
| CADD | 0.952 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.34%
African / African-American · 2,503/75,040 alleles
Filtering AF
3.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.18%
Overall
0.184%
2,963/1,614,210 alleles · low-frequency
exomes 1,514/1,461,894 · genomes 1,449/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.34% | 30 |
| Middle Eastern | 0.528% | 189 |
| Remaining individualsnot grpmax-eligible | 0.259% | 386 |
| Admixed American | 0.192% | 522 |
| European (non-Finnish) | 0.012% | 8,310 |
| South Asian | 0.00768% | 13,013 |
| East Asian | 0.00223% | 44,882 |
| Finnishnot grpmax-eligible | 0.00156% | 64,040 |
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.His200=
- Coding
- c.600C>T
- MANE Select
- NM_019023
- dbSNP
- rs138720818
- Type
- single nucleotide variant
- Location
- chr16:68339417 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 200
- the sam-dependent mtase prmt-type 1 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-his200 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown