Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Common
common (popmax 25.7%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
2
Inborn genetic diseases
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 2.8 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 8.629 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
25.7%
African / African-American · 19,233/74,772 alleles
Filtering AF
25.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 25.3%
Overall
2.34%
37,691/1,613,606 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 25.7% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 5.81% | 17 |
| Middle Eastern | 4.42% | 23 |
| Remaining individualsnot grpmax-eligible | 3.28% | 30 |
| Admixed American | 2.63% | 38 |
| East Asian | 2.07% | 48 |
| South Asian | 1.2% | 83 |
| European (non-Finnish) | 0.907% | 110 |
| Finnishnot grpmax-eligible | 0.178% | 561 |
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
- CREBBP
- Protein
- p.Asp313=
- Coding
- c.939T>C
- MANE Select
- NM_004380
- dbSNP
- rs3025702
- Type
- single nucleotide variant
- Location
- chr16:3810639 (GRCh38)
- Gene constraint
- LOEUF 0.101 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 54.31 · 144 PDB
- Residue 313
- the 'interaction with srcap' region
Similar variants
- CREBBP p.Asp313Gly Uncertain significance ⚠ same residue
- CREBBP c.2881-13G>A Pathogenic/Likely pathogenic ★★ same condition
- CREBBP c.3779+1G>A Pathogenic ★★ same condition
- CREBBP c.3779+1G>T Pathogenic ★★ same condition
- CREBBP c.3836+1G>A Pathogenic ★★ same condition
- CREBBP p.Arg1103Ter Pathogenic ★★ same condition
- CREBBP p.Arg1233Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CREBBP p.Arg1498Ter Pathogenic ★★ same condition
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/crebbp-p-asp313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown