RELB p.Thr494=
c.1482G>A · rs902912356 · VCV2894968
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
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 -1.8 | GERP -4.3 |
| Overall | ||
| CADD | 5.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,074 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000868%
14/1,613,308 alleles · very rare
exomes 14/1,461,082 · genomes 0/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,358 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,466 |
| European (non-Finnish) | 0.000848% | 117,974 |
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.Thr494=
- Coding
- c.1482G>A
- MANE Select
- NM_006509
- dbSNP
- rs902912356
- Type
- single nucleotide variant
- Location
- chr19:45037532 (GRCh38)
- Gene constraint
- LOEUF 0.512 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 70.42 · 1 PDB
- Residue 494
- a UniProt-annotated variant site (in imd53)
Similar variants
- RELB p.Thr494Met Uncertain significance ★★ ⚠ same residue
- RELB p.Thr494Ala Uncertain significance ★ ⚠ same residue
- 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
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-thr494 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown