DCHS2 p.Pro2800=
c.8400G>A · rs114015145 · VCV3041244
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.48%, afr)
Conditions
1
DCHS2-related disorder
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 0.37 | GERP -4.3, phastCons 0.63 |
| Overall | ||
| CADD | 6.935 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.48%
African / African-American · 1,859/75,014 alleles
Filtering AF
2.38%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.35%
Overall
0.135%
2,175/1,613,936 alleles · low-frequency
exomes 1,151/1,461,720 · genomes 1,024/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.48% | 40 |
| Ashkenazi Jewishnot grpmax-eligible | 0.196% | 510 |
| Remaining individualsnot grpmax-eligible | 0.158% | 631 |
| Middle Eastern | 0.132% | 757 |
| Admixed American | 0.122% | 822 |
| South Asian | 0.0132% | 7,590 |
| East Asian | 0.00892% | 11,214 |
| European (non-Finnish) | 0.00508% | 19,666 |
| Finnishnot grpmax-eligible | 0.00313% | 31,984 |
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.Pro2800=
- Coding
- c.8400G>A
- MANE Select
- NM_001358235
- dbSNP
- rs114015145
- Type
- single nucleotide variant
- Location
- chr4:154236252 (GRCh38)
- Gene constraint
- LOEUF 0.909 · pLI <0.01 (gnomAD)
- Residue 2800
- the cadherin 26 domain
Disease context
DCHS2-related disorder
Similar variants
- DCHS2 c.2477-1G>T Uncertain significance ★ same condition
- DCHS2 p.Ala952Thr Uncertain significance same condition
- DCHS2 p.Ile802Val Uncertain significance ⚠ same condition
- DCHS2 p.Ser1397Phe Uncertain significance ⚠ same condition
- DCHS2 c.2053-13755G>A Likely benign same condition
- DCHS2 c.2053-13815C>T Benign same condition
- DCHS2 c.2244+3329T>C Benign same condition
- DCHS2 c.2477-8381C>T Benign same condition
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-pro2800 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown