RAG2 p.Ser470Ter
c.1409C>G · VCV3257398
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 | escapes | premature termination codon in the last exon (2 of 2) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 10 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 39.0 | 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
- RAG2
- Protein
- p.Ser470Ter
- Coding
- c.1409C>G
- MANE Select
- NM_000536
- Type
- single nucleotide variant
- Location
- chr11:36592760 (GRCh38)
- Gene constraint
- LOEUF 0.733 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 75.98 · 1 PDB
- Residue 470
- an α-helix
Similar variants
- RAG2 p.Arg229Gln Pathogenic ★★★ ⚠ same type
- RAG2 p.Arg229Trp Pathogenic ★★★ ⚠ same type
- RAG2 p.Arg39Gly Pathogenic ★★★ ⚠ same type
- RAG2 p.Arg73Cys Likely pathogenic ★★★ ⚠ same type
- RAG2 p.Asp65Tyr Likely pathogenic ★★★ ⚠ same type
- RAG2 p.Cys446Trp Likely pathogenic ★★★ same type
- RAG2 p.Glu437Lys Likely pathogenic ★★★ ⚠ same type
- RAG2 p.Gly319Ter Likely pathogenic ★★★ 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/rag2-p-ser470ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown