PRMT7 p.Ser33Ter
c.98C>A · rs2151436426 · VCV1323497
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
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. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 19 |
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 44.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- PRMT7
- Protein
- p.Ser33Ter
- Coding
- c.98C>A
- MANE Select
- NM_019023
- dbSNP
- rs2151436426
- Type
- single nucleotide variant
- Location
- chr16:68321428 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.19
- Residue 33
- the sam-dependent mtase prmt-type 1 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-ser33ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown