RELB p.Ser390=
c.1170C>T · rs139280106 · VCV1353000
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.8 | GERP -4.6 |
| Overall | ||
| CADD | 13.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
South Asian · 15/90,162 alleles
Filtering AF
0.0102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00829%
Overall
0.00417%
67/1,607,838 alleles · ultra-rare
exomes 61/1,455,546 · genomes 6/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0166% | 6,011 |
| Remaining individualsnot grpmax-eligible | 0.00482% | 20,742 |
| European (non-Finnish) | 0.00391% | 25,600 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0034% | 29,388 |
| East Asian | 0.00224% | 44,554 |
| Admixed American | 0.00169% | 58,998 |
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
- RELB
- Protein
- p.Ser390=
- Coding
- c.1170C>T
- MANE Select
- NM_006509
- dbSNP
- rs139280106
- Type
- single nucleotide variant
- Location
- chr19:45032712 (GRCh38)
- Gene constraint
- LOEUF 0.512 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 70.42 · 1 PDB
- Residue 390
- the rhd domain
Similar variants
- RELB p.Ala541Asp Uncertain significance ★★ ⚠ same type
- RELB p.Ala565Val Uncertain significance ★★ ⚠ same type
- RELB p.Arg176Gln Uncertain significance ★★ ⚠ same type
- RELB p.Arg211Gln Uncertain significance ★★ ⚠ same type
- RELB p.Arg213Gln Uncertain significance ★★ ⚠ same type
- RELB p.Arg213Trp Uncertain significance ★★ ⚠ same type
- RELB p.Arg219Gln Uncertain significance ★★ ⚠ same type
- RELB p.Arg241Trp 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/relb-p-ser390 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown