DCHS2 p.Ser2387=
c.7161T>C · rs41280475 · VCV3039121
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.62%, 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 3 | GERP -4.7, phastCons 1 |
| Overall | ||
| CADD | 1.414 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.62%
Middle Eastern · 159/6,058 alleles
Filtering AF
2.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.16%
Overall
0.7%
11,299/1,613,926 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.62% | 38 |
| Ashkenazi Jewishnot grpmax-eligible | 2.39% | 42 |
| Remaining individualsnot grpmax-eligible | 0.923% | 108 |
| Admixed American | 0.84% | 119 |
| European (non-Finnish) | 0.734% | 136 |
| South Asian | 0.502% | 199 |
| African / African-American | 0.183% | 548 |
| Finnishnot grpmax-eligible | 0.158% | 634 |
| East Asian | 0.00223% | 44,842 |
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
- DCHS2
- Protein
- p.Ser2387=
- Coding
- c.7161T>C
- MANE Select
- NM_001358235
- dbSNP
- rs41280475
- Type
- single nucleotide variant
- Location
- chr4:154240735 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Residue 2387
- the cadherin 22 domain
Similar variants
- DCHS2 c.2053-13744T>A Uncertain significance ★ same type
- DCHS2 c.2053-13798T>C Uncertain significance ★ same type
- DCHS2 c.2053-13820G>A Uncertain significance ★ same type
- DCHS2 c.2053-13834C>G Uncertain significance ★ same type
- DCHS2 c.2244+3317A>T Uncertain significance ★ same type
- DCHS2 c.2476+8901A>C Uncertain significance ★ same type
- DCHS2 c.2477-1G>T Uncertain significance ★ same type
- DCHS2 c.3730+872C>T 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/dchs2-p-ser2387 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown