CDAN1 p.Pro562=
c.1686C>G · rs142013998 · VCV2079031
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0427%, afr)
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 -0.61 | GERP -4.3 |
| Overall | ||
| CADD | 5.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0427%
African / African-American · 32/74,930 alleles
Filtering AF
0.031%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0271%
Overall
0.00266%
43/1,613,884 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0427% | 2,342 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| South Asian | 0.0011% | 91,072 |
| European (non-Finnish) | 0.000254% | 393,298 |
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.Pro562=
- Coding
- c.1686C>G
- MANE Select
- NM_138477
- dbSNP
- rs142013998
- Type
- single nucleotide variant
- Location
- chr15:42731673 (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 562
- an α-helix
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-pro562 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown