CRELD1 p.Pro11=
c.33A>G · rs760082913 · VCV700490
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, nfe)
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 0.12 | GERP 1, phastCons 0.001 |
| Overall | ||
| CADD | 7.106 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
European (non-Finnish) · 26/1,179,974 alleles
Filtering AF
0.00153%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0013%
Overall
0.00174%
28/1,613,818 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0022% | 45,384 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
| African / African-American | 0.00134% | 74,870 |
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
- CRELD1
- Protein
- p.Pro11=
- Coding
- c.33A>G
- MANE Select
- NM_001077415
- dbSNP
- rs760082913
- Type
- single nucleotide variant
- Location
- chr3:9934471 (GRCh38)
- Gene constraint
- LOEUF 0.885 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.68
Similar variants
- CRELD1 c.460+1G>A Likely pathogenic ★★ same type
- CRELD1 c.1049-283C>T Uncertain significance ★★ same type
- CRELD1 c.1049-376T>G Uncertain significance ★★ same type
- CRELD1 c.1049-401C>T Uncertain significance ★★ same type
- CRELD1 p.Arg107Cys Uncertain significance ★★ ⚠ same type
- CRELD1 p.Arg175Gln Uncertain significance ★★ ⚠ same type
- CRELD1 p.Asn72Ser Uncertain significance ★★ ⚠ same type
- CRELD1 p.Cys221Arg 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/creld1-p-pro11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown