DSCAM p.Ala1199=
c.3597G>A · VCV3778079
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0507%, afr)
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 -14 | GERP -3.5 |
| Overall | ||
| CADD | 4.554 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0507%
African / African-American · 38/74,966 alleles
Filtering AF
0.038%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0334%
Overall
0.018%
291/1,613,890 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0507% | 1,973 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,465 |
| European (non-Finnish) | 0.019% | 5,268 |
| Admixed American | 0.00833% | 12,004 |
| South Asian | 0.00769% | 13,010 |
| East Asian | 0.00446% | 22,398 |
| Finnishnot grpmax-eligible | 0.00156% | 63,960 |
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
- DSCAM
- Protein
- p.Ala1199=
- Coding
- c.3597G>A
- MANE Select
- NM_001389
- Type
- single nucleotide variant
- Location
- chr21:40124294 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.98 · 1 PDB
- Residue 1199
- the fibronectin type-iii 4 domain
Similar variants
- DSCAM p.Ala1199Val Uncertain significance ★ ⚠ same residue
- DSCAM p.Ser682Arg Uncertain significance ★★ ⚠ same type
- DSCAM c.5383+9T>A Benign ★★ same type
- DSCAM p.Ala153= Benign ★★ same type
- DSCAM p.Arg1798= Benign/Likely benign ★★ same type
- DSCAM p.Asn1250= Benign ★★ same type
- DSCAM p.Asn576= Benign/Likely benign ★★ same type
- DSCAM p.Asp185= Benign/Likely benign ★★ 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/dscam-p-ala1199 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown