CDAN1 p.Leu166=
c.498G>A · rs376335465 · VCV2963814
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00644%, 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 0.86 | GERP 0.83, phastCons 0.091 |
| Overall | ||
| CADD | 7.422 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00644%
European (non-Finnish) · 76/1,179,932 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00482%
Overall
0.00502%
81/1,613,582 alleles · very rare
exomes 75/1,461,422 · genomes 6/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00644% | 15,525 |
| African / African-American | 0.004% | 24,978 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,230 |
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.Leu166=
- Coding
- c.498G>A
- MANE Select
- NM_138477
- dbSNP
- rs376335465
- Type
- single nucleotide variant
- Location
- chr15:42736373 (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 166
- the 'disordered' region
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-leu166 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown