CREB3L1 p.Pro9=
c.27G>A · rs373536954 · VCV1960966
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0177%, afr)
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 |
|---|---|---|
| Pangolin | Δ0.24 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.16 | GERP -2.5, phastCons 0.84 |
| Overall | ||
| CADD | 11.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0177%
African / African-American · 13/73,654 alleles
Filtering AF
0.0104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00825%
Overall
0.00109%
17/1,564,784 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0177% | 5,666 |
| Admixed American | 0.00563% | 17,755 |
| European (non-Finnish) | 8.66e-05% | 1,154,810 |
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.Pro9=
- Coding
- c.27G>A
- MANE Select
- NM_052854
- dbSNP
- rs373536954
- Type
- single nucleotide variant
- Location
- chr11:46278138 (GRCh38)
- Gene constraint
- LOEUF 0.954 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 55.66
- Residue 9
- 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-pro9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown