DCHS1 p.Ala2289=
c.6867G>A · rs144165467 · VCV2171544
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, mid)
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 -1.2 | GERP -3.2, phastCons 0.002 |
| Overall | ||
| CADD | 5.688 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
Middle Eastern · 2/6,002 alleles
Filtering AF
0.00587%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00244%
Overall
0.00274%
44/1,603,086 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0333% | 3,001 |
| Remaining individualsnot grpmax-eligible | 0.00647% | 15,466 |
| African / African-American | 0.00538% | 18,584 |
| European (non-Finnish) | 0.00281% | 35,590 |
| East Asian | 0.00224% | 44,728 |
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
- DCHS1
- Protein
- p.Ala2289=
- Coding
- c.6867G>A
- MANE Select
- NM_003737
- dbSNP
- rs144165467
- Type
- single nucleotide variant
- Location
- chr11:6625477 (GRCh38)
- Gene constraint
- LOEUF 0.491 · pLI 0.33 · ClinGen HI 1/3 (gnomAD)
- Residue 2289
- the cadherin 22 domain
Similar variants
- DCHS1 p.Ala2289Val Uncertain significance ★ ⚠ same residue
- DCHS1 p.Arg2141Ter Pathogenic/Likely pathogenic ★★ same type
- DCHS1 p.Arg2330Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- DCHS1 p.Ala1241Val Uncertain significance ★★ same type
- DCHS1 p.Ala1325Ser Uncertain significance ★★ ⚠ same type
- DCHS1 p.Ala142Thr Uncertain significance ★★ ⚠ same type
- DCHS1 p.Ala1454Val Uncertain significance ★★ ⚠ same type
- DCHS1 p.Ala1460Pro Uncertain significance ★★ 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/dchs1-p-ala2289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown