CDAN1 p.Val13=
c.39G>A · VCV4799362
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0842%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.57 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.8 | GERP 0.56, phastCons 1 |
| Overall | ||
| CADD | 20.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0842%
Middle Eastern · 5/5,936 alleles
Filtering AF
0.0332%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0215%
Overall
0.00104%
16/1,541,556 alleles · ultra-rare
exomes 16/1,389,470 · genomes 0/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0842% | 1,187 |
| Admixed American | 0.00197% | 50,760 |
| Remaining individualsnot grpmax-eligible | 0.00168% | 59,402 |
| European (non-Finnish) | 0.000787% | 126,993 |
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.Val13=
- Coding
- c.39G>A
- MANE Select
- NM_138477
- Type
- single nucleotide variant
- Location
- chr15:42737064 (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.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
- CDAN1 p.Pro51Leu Likely pathogenic ★★ ⚠ same type
- CDAN1 p.Pro672Leu 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-val13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown