DCDC1 p.Thr239=
c.717G>A · rs773867458 · VCV2039560
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
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 -4.9 | GERP -5.6 |
| Overall | ||
| CADD | 1.815 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,956 alleles
Filtering AF
0.00544%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00381%
Overall
0.000744%
12/1,613,586 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,565 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,474 |
| European (non-Finnish) | 0.000339% | 294,945 |
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.Thr239=
- Coding
- c.717G>A
- MANE Select
- NM_001387274
- dbSNP
- rs773867458
- Type
- single nucleotide variant
- Location
- chr11:31305652 (GRCh38)
- Gene constraint
- LOEUF 1.093 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.53
- Residue 239
- the doublecortin 1 domain
Similar variants
- DCDC1 p.Thr239Met Uncertain significance ★★ ⚠ same residue
- DCDC1 p.Gln95His 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.Glu200= Benign ★★ same type
- DCDC1 p.Leu224= Benign ★★ same type
- DCDC1 p.Lys1494Arg 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-thr239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown