DCDC1 p.Ala731=
c.2193T>C · rs150056724 · VCV3041707
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.775%, nfe)
Conditions
1
DCDC1-related disorder
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 -1.8 | GERP -4.4 |
| Overall | ||
| CADD | 1.555 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.775%
European (non-Finnish) · 3,220/415,594 alleles
Filtering AF
0.752%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.743%
Overall
0.47%
3,581/761,620 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.775% | 129 |
| Amishnot grpmax-eligible | 0.768% | 130 |
| Remaining individualsnot grpmax-eligible | 0.321% | 312 |
| Finnishnot grpmax-eligible | 0.183% | 547 |
| African / African-American | 0.166% | 604 |
| Admixed American | 0.0804% | 1,245 |
| Middle Eastern | 0.0226% | 4,428 |
| South Asian | 0.00681% | 14,689 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00412% | 24,298 |
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.Ala731=
- Coding
- c.2193T>C
- MANE Select
- NM_001387274
- dbSNP
- rs150056724
- Type
- single nucleotide variant
- Location
- chr11:31091437 (GRCh38)
- Gene constraint
- LOEUF 1.093 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.53
- Residue 731
- the ricin b-type lectin 1 domain
Disease context
DCDC1-related disorder
Similar variants
- DCDC1 p.Cys1699Ter Likely pathogenic ★ same condition
- DCDC1 c.164+3A>G Likely benign same condition
- DCDC1 c.1983+10T>C Likely benign same condition
- DCDC1 c.2298+8C>T Benign same condition
- DCDC1 c.2716-10C>A Benign same condition
- DCDC1 c.5233+7A>G Likely benign same condition
- DCDC1 p.Ala684= Likely benign same condition
- DCDC1 p.Arg864Ser Benign same condition
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-ala731 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown