DSCAM p.Ile1332=
c.3996T>C · VCV3389246
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000697%, nfe)
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 3.4 | GERP 0.13, phastCons 1 |
| Overall | ||
| CADD | 9.749 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000697%
European (non-Finnish) · 8/1,147,488 alleles
Filtering AF
0.0003%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000217%
Overall
0.000509%
8/1,570,196 alleles · very rare
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.Ile1332=
- Coding
- c.3996T>C
- MANE Select
- NM_001389
- Type
- single nucleotide variant
- Location
- chr21:40085738 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.98 · 1 PDB
- Residue 1332
- the ig-like c2-type 10 domain; a disulfide bond
Similar variants
- 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
- DSCAM p.Gln582= 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-ile1332 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown