RELA p.Ser536del
c.1603TCC[1] · rs766441250 · VCV2071606
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0168%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.2 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 17.8 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0168%
Admixed American · 10/59,432 alleles
Filtering AF
0.00908%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00687%
Overall
0.00496%
80/1,611,686 alleles · ultra-rare
exomes 75/1,459,484 · genomes 5/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0168% | 5,943 |
| Middle Eastern | 0.0165% | 6,050 |
| East Asian | 0.00892% | 11,209 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,474 |
| African / African-American | 0.00534% | 18,716 |
| European (non-Finnish) | 0.00466% | 21,438 |
| South Asian | 0.0011% | 90,716 |
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
- RELA
- Protein
- p.Ser536del
- Coding
- c.1603TCC[1]
- MANE Select
- NM_021975
- dbSNP
- rs766441250
- Type
- Microsatellite
- Location
- chr11:65654426 (GRCh38)
- Gene constraint
- LOEUF 0.4 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.52 · 88 PDB
- Residue 536
- a modified residue (phosphoserine; by ikkb); a UniProt-annotated variant site (found in a patient diagnosed with autoimmune lymphoproliferative syndrome; uncertain significance); the 'transcriptional activation domain 2' region; a turn
Similar variants
- RELA p.Ser536= Likely benign ★★ same residue
- RELA p.Ser536Cys Uncertain significance ★ ⚠ same residue
- RELA p.Ser203fs Pathogenic ★ same type
- RELA p.Tyr227fs Pathogenic ★ same type
- RELA p.380AP[3] Uncertain significance ★ same type
- RELA p.Asn139del Uncertain significance ★ same type
- RELA c.1034-21CT[2] Likely benign ★ 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/rela-p-ser536del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown