DGCR2 p.Ala511=
c.1533C>T · rs376309095 · VCV740399
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0077%, sas)
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 -9.4 | GERP -2.8 |
| Overall | ||
| CADD | 0.105 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0077%
South Asian · 7/90,938 alleles
Filtering AF
0.00605%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00565%
Overall
0.00627%
101/1,611,738 alleles · very rare
exomes 94/1,459,512 · genomes 7/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0077% | 12,991 |
| European (non-Finnish) | 0.00738% | 13,556 |
| Admixed American | 0.00501% | 19,949 |
| African / African-American | 0.00267% | 37,462 |
| East Asian | 0.00223% | 44,892 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,402 |
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.Ala511=
- Coding
- c.1533C>T
- MANE Select
- NM_005137
- dbSNP
- rs376309095
- Type
- single nucleotide variant
- Location
- chr22:19038985 (GRCh38)
- Gene constraint
- LOEUF 0.686 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.74
- Residue 511
- the 'disordered' region
Similar variants
- 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.Pro439= 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-ala511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown