DCC p.Cys261=
c.783T>C · rs764544614 · VCV2648724
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -3.2 | GERP -3.7 |
| Overall | ||
| CADD | 2.522 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,842 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000277%
Overall
0.000274%
4/1,460,938 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,421 |
| European (non-Finnish) | 0.00017% | 589,657 |
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
- DCC
- Protein
- p.Cys261=
- Coding
- c.783T>C
- MANE Select
- NM_005215
- dbSNP
- rs764544614
- Type
- single nucleotide variant
- Location
- chr18:52923792 (GRCh38)
- Gene constraint
- LOEUF 0.414 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 68.60 · 9 PDB
- Residue 261
- a disulfide bond; the ig-like c2-type 3 domain
Similar variants
- DCC p.Arg1021Ter Pathogenic ★★ same type
- DCC p.Arg1025Ter Pathogenic/Likely pathogenic ★★ same type
- DCC p.Arg275Ter Pathogenic ★★ same type
- DCC p.Arg879Ter Pathogenic/Likely pathogenic ★★ same type
- DCC c.3620-2A>G Uncertain significance ★★ same type
- DCC p.Arg597Gln Uncertain significance ★★ ⚠ same type
- DCC p.Gly1294Arg Uncertain significance ★★ ⚠ same type
- DCC p.Gly55Arg Uncertain significance ★★ ⚠ 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/dcc-p-cys261 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown