CDHR1 p.Phe620=
c.1860C>T · rs374261522 · VCV1158212
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 -8.3 | GERP -2.9 |
| Overall | ||
| CADD | 0.135 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,090 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000496%
8/1,614,114 alleles · very rare
exomes 7/1,461,888 · genomes 1/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,773 |
| East Asian | 0.00223% | 44,900 |
| European (non-Finnish) | 0.000254% | 393,351 |
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.Phe620=
- Coding
- c.1860C>T
- MANE Select
- NM_033100
- dbSNP
- rs374261522
- Type
- single nucleotide variant
- Location
- chr10:84213168 (GRCh38)
- Gene constraint
- LOEUF 1.004 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.79
- Residue 620
- the cadherin 6 domain
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-phe620 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown