DCDC1 p.Glu200=
c.600G>A · rs2616815 · VCV1286561
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 90.4%, afr) — too common for a highly-penetrant pathogenic allele
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 0.12 | GERP -1.2, phastCons 0.004 |
| Overall | ||
| CADD | 6.415 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
90.4%
African / African-American · 67,759/74,952 alleles
Filtering AF
89.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 89.6%
Overall
65%
1,047,831/1,612,494 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 90.4% | 1 |
| Amishnot grpmax-eligible | 77.8% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 73.2% | 1 |
| Middle Eastern | 69.9% | 1 |
| Admixed American | 69% | 1 |
| Remaining individualsnot grpmax-eligible | 65.6% | 2 |
| European (non-Finnish) | 64.6% | 2 |
| South Asian | 62.6% | 2 |
| Finnishnot grpmax-eligible | 55.9% | 2 |
| East Asian | 37.5% | 3 |
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
- DCDC1
- Protein
- p.Glu200=
- Coding
- c.600G>A
- MANE Select
- NM_001387274
- dbSNP
- rs2616815
- Type
- single nucleotide variant
- Location
- chr11:31305769 (GRCh38)
- Gene constraint
- LOEUF 1.093 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.53
- Residue 200
- the doublecortin 1 domain
Similar variants
- DCDC1 p.Gln95His Uncertain significance ★★ ⚠ same type
- DCDC1 p.Thr239Met Uncertain significance ★★ ⚠ same type
- DCDC1 p.Thr317Ala Uncertain significance ★★ ⚠ same type
- DCDC1 c.591+13C>T Benign ★★ same type
- DCDC1 p.Ala1431Thr Benign ★★ ⚠ same type
- DCDC1 p.Leu224= Benign ★★ same type
- DCDC1 p.Lys1494Arg Benign ★★ same type
- DCDC1 p.Ser1701Pro 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/dcdc1-p-glu200 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown