DCHS1 p.Ser86=
c.258C>T · rs534770743 · VCV752079
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.294%, 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 -9.1 | GERP -3.5 |
| Overall | ||
| CADD | 1.394 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.294%
South Asian · 268/91,082 alleles
Filtering AF
0.265%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.254%
Overall
0.0175%
282/1,613,514 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.294% | 340 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,680 |
| Middle Eastern | 0.0165% | 6,058 |
| Admixed American | 0.00167% | 60,026 |
| European (non-Finnish) | 8.48e-05% | 1,179,885 |
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.Ser86=
- Coding
- c.258C>T
- MANE Select
- NM_003737
- dbSNP
- rs534770743
- Type
- single nucleotide variant
- Location
- chr11:6641356 (GRCh38)
- Gene constraint
- LOEUF 0.491 · pLI 0.33 · ClinGen HI 1/3 (gnomAD)
- Residue 86
- the cadherin 1 domain
Similar variants
- 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
- DCHS1 p.Ala1490Glu 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-ser86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown