CDHR1 p.Asn855del
c.2562CAA[1] · rs1242103648 · VCV2069716
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -0.21, phastCons 0.016 |
| Overall | ||
| CADD | 10.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,918 alleles
Overall
0.000657%
1/152,188 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.Asn855del
- Coding
- c.2562CAA[1]
- MANE Select
- NM_033100
- dbSNP
- rs1242103648
- Type
- Microsatellite
- Location
- chr10:84214602 (GRCh38)
- Gene constraint
- LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.79
Similar variants
- CDHR1 p.Asn855= Likely benign ★ same residue
- CDHR1 p.Asp65fs Pathogenic ★★ same type
- CDHR1 p.Asn781del Uncertain significance ★★ same type
- CDHR1 p.Lys851del Likely benign ★★ same type
- CDHR1 p.Leu41fs Pathogenic ★ same type
- CDHR1 c.298-3_298-2del Uncertain significance ★ same type
- CDHR1 p.Phe28del Uncertain significance ★ same type
- CDHR1 c.152-12_152-11del Likely benign ★ 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-asn855del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown