PRMT7 p.Thr599=
c.1797C>T · rs1131933 · VCV1269969
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 79.1%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
1
short stature-brachydactyly-obesity-global developmental delay syndrome
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 0.11 | GERP -4.9 |
| Overall | ||
| CADD | 5.617 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
79.1%
East Asian · 35,285/44,580 alleles
Filtering AF
78.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 78.2%
Overall
46.8%
748,083/1,599,246 alleles · common
exomes 673,413/1,447,126 · genomes 74,670/152,120 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 79.1% | 1 |
| Admixed American | 60.5% | 2 |
| African / African-American | 55.5% | 2 |
| South Asian | 47.7% | 2 |
| Remaining individualsnot grpmax-eligible | 46.1% | 2 |
| European (non-Finnish) | 45% | 2 |
| Finnishnot grpmax-eligible | 40.3% | 2 |
| Amishnot grpmax-eligible | 33.6% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 32.8% | 3 |
| Middle Eastern | 30.9% | 3 |
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.Thr599=
- Coding
- c.1797C>T
- MANE Select
- NM_019023
- dbSNP
- rs1131933
- Type
- single nucleotide variant
- Location
- chr16:68355869 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 599
- the sam-dependent mtase prmt-type 2 domain
Similar variants
- PRMT7 c.1056-1G>T Pathogenic/Likely pathogenic ★★ same condition
- PRMT7 p.Arg274Ter Pathogenic/Likely pathogenic ★★ same condition
- PRMT7 p.Arg390Ter Pathogenic ★★ same condition
- PRMT7 p.Cys571Ter Pathogenic ★★ same condition
- PRMT7 p.Gln323Ter Pathogenic ★★ same condition
- PRMT7 p.Glu108Ter Pathogenic/Likely pathogenic ★★ same condition
- PRMT7 p.Tyr159Ter Pathogenic ★★ same condition
- PRMT7 p.Arg360Cys 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-thr599 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown