DSCAML1 p.Pro226=
c.678C>T · rs143227689 · VCV1559753
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.77%, 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 1.4 | GERP -5.3, phastCons 1 |
| Overall | ||
| CADD | 9.067 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.77%
Middle Eastern · 41/5,326 alleles
Filtering AF
0.583%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.518%
Overall
0.102%
1,604/1,575,102 alleles · rare
exomes 1,486/1,422,776 · genomes 118/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.77% | 130 |
| Ashkenazi Jewishnot grpmax-eligible | 0.288% | 347 |
| South Asian | 0.231% | 432 |
| Remaining individualsnot grpmax-eligible | 0.175% | 571 |
| European (non-Finnish) | 0.0945% | 1,058 |
| Admixed American | 0.0558% | 1,792 |
| Finnishnot grpmax-eligible | 0.0321% | 3,111 |
| African / African-American | 0.0256% | 3,900 |
| East Asian | 0.0163% | 6,133 |
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
- DSCAML1
- Protein
- p.Pro226=
- Coding
- c.678C>T
- MANE Select
- NM_020693
- dbSNP
- rs143227689
- Type
- single nucleotide variant
- Location
- chr11:117525064 (GRCh38)
- Gene constraint
- LOEUF 0.253 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.92 · 1 PDB
- Residue 226
- the ig-like c2-type 3 domain
Similar variants
- DSCAML1 c.-101C>T Uncertain significance ★★ same type
- DSCAML1 c.-17T>C Uncertain significance ★★ same type
- DSCAML1 c.-23G>A Uncertain significance ★★ same type
- DSCAML1 c.-44C>T Uncertain significance ★★ same type
- DSCAML1 c.-51G>T Uncertain significance ★★ same type
- DSCAML1 c.-57G>A Uncertain significance ★★ same type
- DSCAML1 c.-87G>A Uncertain significance ★★ same type
- DSCAML1 p.Ala1060Ser 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/dscaml1-p-pro226 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown