CDHR1 p.Val255=
c.765G>A · VCV4779469
Likely benign
Single submitter
Classification
Likely benign
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 | Δ0.43 | donor loss, 1 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.79 | GERP 3.6, phastCons 1 |
| Overall | ||
| CADD | 5.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,032 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000547%
8/1,461,892 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,032 |
| European (non-Finnish) | 0.000593% | 168,577 |
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.Val255=
- Coding
- c.765G>A
- MANE Select
- NM_033100
- Type
- single nucleotide variant
- Location
- chr10:84203105 (GRCh38)
- Gene constraint
- LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.79
- Residue 255
- the cadherin 3 domain
Similar variants
- CDHR1 p.Val255Glu Uncertain significance ★★ ⚠ same residue
- CDHR1 p.Val255Met Uncertain significance ★ same residue
- 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
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-val255 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown