CDAN1 p.Pro125=
c.375G>A · rs1448409048 · VCV1907800
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 -0.33 | GERP -0.24, phastCons 0.012 |
| Overall | ||
| CADD | 10.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Remaining individualsnot grpmax-eligible | 0.0111% | 9,008 |
| African / African-Americangrpmax | 0.00909% | 11,003 |
| East Asian | 0.00288% | 34,766 |
Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- CDAN1
- Protein
- p.Pro125=
- Coding
- c.375G>A
- MANE Select
- NM_138477
- dbSNP
- rs1448409048
- Type
- single nucleotide variant
- Location
- chr15:42736496 (GRCh38)
- Gene constraint
- LOEUF 0.908 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.58 · 2 PDB
- Residue 125
- the 'disordered' region
Disease context
anemia, congenital dyserythropoietic, type 1a — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Congenital dyserythropoietic anemia type I (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Infancy, Neonatal
- Prevalence
- <1 / 1 000 000 (Europe)
Similar variants
- CDAN1 p.Arg1042Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CDAN1 p.Arg682Ter Pathogenic ★★ same condition
- CDAN1 p.Arg714Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CDAN1 p.Asn599Ser Likely pathogenic ★★ ⚠ same condition
- CDAN1 p.Phe52Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CDAN1 p.Pro1130Leu Pathogenic/Likely pathogenic ★★ same condition
- CDAN1 p.Pro51Leu Likely pathogenic ★★ ⚠ same condition
- CDAN1 p.Pro672Leu Pathogenic/Likely 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/cdan1-p-pro125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown