CDHR1 c.151+6T>C
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
cone-rod dystrophy 15
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +6 | donor splice region (+6, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | Δ0.29 | donor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 0.17 | GERP -2.8, phastCons 0.008 |
| Overall | ||
| CADD | 21.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CDHR1
- Coding
- c.151+6T>C
- MANE Select
- NM_033100
- dbSNP
- rs1842015989
- Type
- single nucleotide variant
- Location
- chr10:84195595 (GRCh38)
- Gene constraint
- LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.79
Disease context
cone-rod dystrophy 15 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Cone rod dystrophy (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, X-linked recessive
- Onset
- Adolescent, Adult, Childhood
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- CDHR1 c.1485+2T>G Pathogenic ★★ same condition
- CDHR1 c.525+1G>A Pathogenic ★★ same condition
- CDHR1 c.56-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CDHR1 c.863-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CDHR1 p.Arg407Ter Pathogenic ★★ same condition
- CDHR1 c.1554-3C>A Uncertain significance ★★ same condition
- CDHR1 c.862+4A>C Uncertain significance ★★ same condition
- CDHR1 p.Arg407Gln Uncertain significance ★★ ⚠ 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-c-151-plus-6t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown