DSCAM p.Val1278=
c.3834C>T · rs62237594 · VCV771938
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.23%, 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 -3.8 | GERP -4.9 |
| Overall | ||
| CADD | 0.323 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.23%
European (non-Finnish) · 26,141/1,173,996 alleles
Filtering AF
2.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.19%
Overall
1.83%
29,152/1,596,108 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 2.23% | 45 |
| Remaining individualsnot grpmax-eligible | 1.71% | 58 |
| Middle Eastern | 1.57% | 64 |
| Ashkenazi Jewishnot grpmax-eligible | 1.33% | 75 |
| Admixed American | 1.06% | 94 |
| Finnishnot grpmax-eligible | 0.551% | 181 |
| African / African-American | 0.328% | 305 |
| South Asian | 0.324% | 308 |
| East Asian | 0.00232% | 43,184 |
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.Val1278=
- Coding
- c.3834C>T
- MANE Select
- NM_001389
- dbSNP
- rs62237594
- Type
- single nucleotide variant
- Location
- chr21:40093737 (GRCh38)
- Gene constraint
- LOEUF 0.28 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.98 · 1 PDB
- Residue 1278
- the fibronectin type-iii 4 domain
Similar variants
- DSCAM p.Val1278Ile 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-val1278 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown