CDHR1 p.Ser490fs
c.1467_1468insCG · VCV4908381
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
CDHR1-related disorders
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 13 of 17 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP 1.5, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDHR1
- Protein
- p.Ser490fs
- Coding
- c.1467_1468insCG
- MANE Select
- NM_033100
- Type
- Insertion
- Location
- chr10:84211147 (GRCh38)
- Gene constraint
- LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.79
- Residue 490
- the cadherin 5 domain
Disease context
CDHR1-related disorders
Similar variants
- CDHR1 p.Ser490= Conflicting classifications of pathogenicity ★ same residue
- CDHR1 c.1168-1G>C Pathogenic/Likely pathogenic ★★ same condition
- CDHR1 c.1321-1G>A Likely pathogenic ★★ same condition
- CDHR1 c.1485+2T>C Pathogenic ★★ same condition
- CDHR1 c.1485+2T>G Pathogenic ★★ same condition
- CDHR1 c.1554-2A>C Pathogenic/Likely pathogenic ★★ same condition
- CDHR1 c.297+1G>T Pathogenic ★★ same condition
- CDHR1 c.526-1G>A Likely pathogenic ★★ same condition
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-ser490fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown