DSCAM p.Tyr1818=
c.5454C>T · rs199512904 · VCV2652669
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0428%, sas)
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 -1.6 | GERP -5.1 |
| Overall | ||
| CADD | 4.237 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0428%
South Asian · 39/91,082 alleles
Filtering AF
0.0322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0284%
Overall
0.0241%
389/1,614,084 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0428% | 2,335 |
| Finnishnot grpmax-eligible | 0.0297% | 3,368 |
| European (non-Finnish) | 0.0252% | 3,973 |
| Admixed American | 0.02% | 5,002 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| African / African-American | 0.00933% | 10,716 |
| East Asian | 0.00669% | 14,951 |
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.Tyr1818=
- Coding
- c.5454C>T
- MANE Select
- NM_001389
- dbSNP
- rs199512904
- Type
- single nucleotide variant
- Location
- chr21:40042603 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.98 · 1 PDB
- Residue 1818
- the 'required for netrin-mediated axon repulsion of neuronal growth cones' region
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-tyr1818 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown