RELT p.Pro201=
c.603C>T · rs150760056 · VCV3037256
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.728%, sas)
Conditions
1
RELT-related disorder
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 -5.3 | GERP -4.4 |
| Overall | ||
| CADD | 2.808 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.728%
South Asian · 663/91,078 alleles
Filtering AF
0.682%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.664%
Overall
0.515%
8,312/1,612,926 alleles · rare
exomes 7,774/1,460,638 · genomes 538/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.728% | 137 |
| European (non-Finnish) | 0.593% | 169 |
| Remaining individualsnot grpmax-eligible | 0.479% | 209 |
| Middle Eastern | 0.297% | 337 |
| Finnishnot grpmax-eligible | 0.182% | 548 |
| Ashkenazi Jewishnot grpmax-eligible | 0.176% | 569 |
| Admixed American | 0.15% | 667 |
| African / African-American | 0.0986% | 1,014 |
| East Asian | 0.00891% | 11,218 |
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
- RELT
- Protein
- p.Pro201=
- Coding
- c.603C>T
- MANE Select
- NM_152222
- dbSNP
- rs150760056
- Type
- single nucleotide variant
- Location
- chr11:73392446 (GRCh38)
- Gene constraint
- LOEUF 0.955 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.38
Disease context
RELT-related disorder
Similar variants
- RELT p.Ala314= Likely benign same condition
- RELT p.Arg338Pro Likely benign same condition
- RELT p.Met363Val Benign same condition
- RELT p.Thr256Met Benign same condition
- RELT p.Thr360= Benign same condition
- RELT p.Val367= Benign same condition
- RELT p.Val367Glu Benign same condition
- RELT p.Ala160= 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/relt-p-pro201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown