CDHR1 p.Ala706=
c.2118C>T · rs144898105 · VCV1145861
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0374%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -6.9 |
| Overall | ||
| CADD | 0.782 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0374%
African / African-American · 28/74,922 alleles
Filtering AF
0.0265%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0229%
Overall
0.00198%
32/1,614,030 alleles · ultra-rare
exomes 19/1,461,842 · genomes 13/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0374% | 2,676 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.000254% | 393,349 |
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.Ala706=
- Coding
- c.2118C>T
- MANE Select
- NM_033100
- dbSNP
- rs144898105
- Type
- single nucleotide variant
- Location
- chr10:84214159 (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 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-ala706 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown