DSCAML1 p.Pro89=
c.267C>T · rs766271261 · VCV2186763
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.13%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 11.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.13%
East Asian · 56/43,218 alleles
Filtering AF
0.102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0927%
Overall
0.00657%
104/1,583,230 alleles · rare
exomes 89/1,430,884 · genomes 15/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.13% | 772 |
| South Asian | 0.0357% | 2,801 |
| Middle Eastern | 0.0167% | 5,988 |
| Remaining individualsnot grpmax-eligible | 0.0131% | 7,661 |
| African / African-American | 0.00135% | 73,924 |
| European (non-Finnish) | 0.000602% | 166,167 |
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.Pro89=
- Coding
- c.267C>T
- MANE Select
- NM_020693
- dbSNP
- rs766271261
- Type
- single nucleotide variant
- Location
- chr11:117780590 (GRCh38)
- Gene constraint
- LOEUF 0.253 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.92 · 1 PDB
- Residue 89
- the ig-like c2-type 1 domain
Similar variants
- DSCAML1 p.Pro89Ala Uncertain significance ★★ ⚠ same residue
- 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
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-pro89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown