CREB3L1 p.Pro15=
c.45C>T · rs2496076659 · VCV3002281
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00236%, eas)
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 -1.5 | GERP -1.4 |
| Overall | ||
| CADD | 11.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00236%
East Asian · 1/42,294 alleles
Filtering AF
2.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000254%
4/1,574,362 alleles · very rare
exomes 4/1,422,028 · genomes 0/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00236% | 42,294 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 60,988 |
| European (non-Finnish) | 0.000172% | 580,026 |
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
- CREB3L1
- Protein
- p.Pro15=
- Coding
- c.45C>T
- MANE Select
- NM_052854
- dbSNP
- rs2496076659
- Type
- single nucleotide variant
- Location
- chr11:46278156 (GRCh38)
- Gene constraint
- LOEUF 0.954 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.66
- Residue 15
- the 'required for transcriptional activation' region
Similar variants
- CREB3L1 p.Ala151Ser Uncertain significance ★★ ⚠ same type
- CREB3L1 p.Ala369Thr Uncertain significance ★★ ⚠ same type
- CREB3L1 p.Ala95Val Uncertain significance ★★ ⚠ same type
- CREB3L1 p.Arg223Cys Uncertain significance ★★ ⚠ same type
- CREB3L1 p.Arg236His Uncertain significance ★★ ⚠ same type
- CREB3L1 p.Arg268Trp Uncertain significance ★★ ⚠ same type
- CREB3L1 p.Arg308Cys Uncertain significance ★★ ⚠ same type
- CREB3L1 p.Arg462Trp 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/creb3l1-p-pro15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown