CDAN1 p.Pro954=
c.2862G>A · rs747935657 · VCV2040794
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
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 -13 | GERP -4.4 |
| Overall | ||
| CADD | 0.198 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,010 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.0018%
29/1,613,586 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 10,002 |
| European (non-Finnish) | 0.00178% | 56,189 |
| African / African-American | 0.00133% | 74,926 |
| South Asian | 0.0011% | 91,086 |
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.Pro954=
- Coding
- c.2862G>A
- MANE Select
- NM_138477
- dbSNP
- rs747935657
- Type
- single nucleotide variant
- Location
- chr15:42728210 (GRCh38)
- Gene constraint
- LOEUF 0.908 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.58 · 2 PDB
Similar variants
- CDAN1 p.Pro954Leu Uncertain significance ★★ ⚠ same residue
- CDAN1 p.Pro954Ser Uncertain significance ★ ⚠ same residue
- CDAN1 p.Arg1042Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- CDAN1 p.Arg682Ter Pathogenic ★★ same type
- CDAN1 p.Arg714Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- CDAN1 p.Asn599Ser Likely pathogenic ★★ ⚠ same type
- CDAN1 p.Phe52Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- CDAN1 p.Pro1130Leu Pathogenic/Likely pathogenic ★★ 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/cdan1-p-pro954 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown