DSCAM p.Pro1313=
c.3939T>C · rs2517009347 · VCV3049289
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000339%, nfe)
Conditions
1
DSCAM-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 -1 | GERP -4.9 |
| Overall | ||
| CADD | 3.773 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,179,572 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,613,654 alleles · very rare
exomes 4/1,461,330 · genomes 0/152,324 · joint denominator
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.Pro1313=
- Coding
- c.3939T>C
- MANE Select
- NM_001389
- dbSNP
- rs2517009347
- Type
- single nucleotide variant
- Location
- chr21:40087199 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.98 · 1 PDB
- Residue 1313
- the ig-like c2-type 10 domain
Disease context
DSCAM-related disorder
Similar variants
- DSCAM p.Arg388Leu Uncertain significance ★ ⚠ same condition
- DSCAM p.Gly1976Arg Uncertain significance ★ ⚠ same condition
- DSCAM p.Lys1283Asn Uncertain significance ★ ⚠ same condition
- DSCAM p.Lys391Arg Uncertain significance ★ ⚠ same condition
- DSCAM p.Met1548Ile Uncertain significance ★ ⚠ same condition
- DSCAM p.Thr485Ile Uncertain significance ★ ⚠ same condition
- DSCAM c.5036-2A>G Uncertain significance same condition
- DSCAM p.Arg1657Ter Uncertain significance 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/dscam-p-pro1313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown