GLUL p.Arg280=
c.838C>A · rs775139524 · VCV2681299
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Conditions
1
EBV-positive nodal T- and NK-cell lymphoma
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 0.42 | GERP -0.016, phastCons 0.99 |
| Overall | ||
| CADD | 8.764 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,896 alleles
Overall
6.2e-05%
1/1,613,986 alleles · very rare
exomes 1/1,461,742 · genomes 0/152,244 · joint denominator
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
- GLUL
- Protein
- p.Arg280=
- Coding
- c.838C>A
- MANE Select
- NM_001033044
- dbSNP
- rs775139524
- Type
- single nucleotide variant
- Location
- chr1:182384689 (GRCh38)
- Gene constraint
- LOEUF 0.377 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 97.58 · 12 PDB
- Residue 280
- the gs catalytic domain
Disease context
EBV-positive nodal T- and NK-cell lymphoma
Similar variants
- GLUL p.Met1Ile Uncertain significance ★★ same condition
- GLUL p.Arg280fs Uncertain significance ★ same residue
- GLUL c.167-6C>G Likely benign same condition
- GLUL p.Asn152= Likely benign same condition
- GLUL p.Thr358= Likely benign same condition
- GLUL p.Arg106Gln Uncertain significance ★ same condition
- GLUL p.Met1Val Pathogenic/Likely pathogenic ★★ same type
- GLUL c.*129G>T 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/glul-p-arg280 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown