DGCR2 p.Pro439=
c.1317G>A · rs146218436 · VCV773616
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.726%, 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 -12 | GERP -3.5 |
| Overall | ||
| CADD | 1.586 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.726%
European (non-Finnish) · 8,565/1,179,948 alleles
Filtering AF
0.713%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.708%
Overall
0.592%
9,548/1,613,976 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.726% | 138 |
| Finnishnot grpmax-eligible | 0.486% | 206 |
| Remaining individualsnot grpmax-eligible | 0.405% | 247 |
| South Asian | 0.27% | 370 |
| Admixed American | 0.17% | 588 |
| Middle Eastern | 0.0825% | 1,212 |
| African / African-American | 0.0733% | 1,364 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0304% | 3,288 |
| East Asian | 0.00446% | 22,426 |
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
- DGCR2
- Protein
- p.Pro439=
- Coding
- c.1317G>A
- MANE Select
- NM_005137
- dbSNP
- rs146218436
- Type
- single nucleotide variant
- Location
- chr22:19041137 (GRCh38)
- Gene constraint
- LOEUF 0.686 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.74
Similar variants
- DGCR2 p.Pro439Leu Uncertain significance ★ ⚠ same residue
- DGCR2 p.Arg74His Uncertain significance ★★ ⚠ same type
- DGCR2 p.Val102Met Uncertain significance ★★ ⚠ same type
- DGCR2 p.Ala141= Benign ★★ same type
- DGCR2 p.Leu11= Benign/Likely benign ★★ same type
- DGCR2 p.Ala142Glu Uncertain significance ★ ⚠ same type
- DGCR2 p.Ala153Thr Uncertain significance ★ ⚠ same type
- DGCR2 p.Ala469Gly 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/dgcr2-p-pro439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown