DCDC2C p.Ala301=
c.903G>A · rs557310721 · VCV2650639
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.08%, nfe)
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 -20 | GERP -5 |
| Overall | ||
| CADD | 0.159 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.08%
European (non-Finnish) · 918/1,146,980 alleles
Filtering AF
0.0757%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.074%
Overall
0.0647%
1,004/1,550,606 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.08% | 1,249 |
| Remaining individualsnot grpmax-eligible | 0.0516% | 1,940 |
| Middle Eastern | 0.0334% | 2,996 |
| South Asian | 0.0286% | 3,503 |
| Admixed American | 0.0235% | 4,250 |
| African / African-American | 0.0219% | 4,572 |
| East Asian | 0.00244% | 40,930 |
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
- DCDC2C
- Protein
- p.Ala301=
- Coding
- c.903G>A
- MANE Select
- NM_001287444
- dbSNP
- rs557310721
- Type
- single nucleotide variant
- Location
- chr2:3769360 (GRCh38)
- Gene constraint
- LOEUF 1.498 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.53
Similar variants
- DCDC2C c.955-1G>C Uncertain significance ★ same type
- DCDC2C p.Tyr21Cys Likely 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/dcdc2c-p-ala301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown