DCDC2 p.Thr289=
c.867G>A · VCV4973895
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0107%, afr)
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 -3.1 | GERP -3.5 |
| Overall | ||
| CADD | 0.694 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0107%
African / African-American · 8/74,878 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.00161%
26/1,613,364 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0107% | 9,360 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,823 |
| South Asian | 0.00439% | 22,755 |
| Admixed American | 0.00334% | 29,967 |
| East Asian | 0.00223% | 44,870 |
| European (non-Finnish) | 0.000678% | 147,455 |
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
- DCDC2
- Protein
- p.Thr289=
- Coding
- c.867G>A
- MANE Select
- NM_016356
- Type
- single nucleotide variant
- Location
- chr6:24278104 (GRCh38)
- Gene constraint
- LOEUF 1.062 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.93 · 1 PDB
- Residue 289
- a UniProt-annotated variant site (in nsc); the 'disordered' region
Similar variants
- DCDC2 p.Thr289Met Uncertain significance ★ ⚠ same residue
- DCDC2 c.294-2A>G Pathogenic ★★ same type
- DCDC2 c.349-2A>G Pathogenic ★★ same type
- DCDC2 c.705-2A>G Pathogenic ★★ same type
- DCDC2 p.Leu297Ter Pathogenic ★★ same type
- DCDC2 p.Met1Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
- DCDC2 p.Ser128Ter Pathogenic/Likely pathogenic ★★ same type
- DCDC2 p.Ala153Gly 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/dcdc2-p-thr289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown