CDHR1 p.Ala182=
c.546C>A · rs747165743 · VCV1382511
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ1.00 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.83 | gain · loss 0.63 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -6.4 |
| Overall | ||
| CADD | 17.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,026 alleles
Overall
6.86e-05%
1/1,458,154 alleles · very rare
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
- CDHR1
- Protein
- p.Ala182=
- Coding
- c.546C>A
- MANE Select
- NM_033100
- dbSNP
- rs747165743
- Type
- single nucleotide variant
- Location
- chr10:84201827 (GRCh38)
- Gene constraint
- LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.79
- Residue 182
- the cadherin 2 domain
Similar variants
- CDHR1 c.1168-1G>C Pathogenic/Likely pathogenic ★★ same type
- CDHR1 c.1321-1G>A Likely pathogenic ★★ same type
- CDHR1 c.1485+2T>C Pathogenic ★★ same type
- CDHR1 c.1485+2T>G Pathogenic ★★ same type
- CDHR1 c.1554-2A>C Pathogenic/Likely pathogenic ★★ same type
- CDHR1 c.297+1G>T Pathogenic ★★ same type
- CDHR1 c.525+1G>A Pathogenic ★★ same type
- CDHR1 c.526-1G>A 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/cdhr1-p-ala182 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown