DLGAP1 p.Pro824=
c.2472C>T · rs73939849 · VCV788613
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.29%, afr)
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 -16 | GERP -5.3 |
| Overall | ||
| CADD | 0.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.29%
African / African-American · 970/74,984 alleles
Filtering AF
1.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.2%
Overall
0.0748%
1,207/1,612,882 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.29% | 77 |
| Middle Eastern | 0.149% | 672 |
| Admixed American | 0.118% | 845 |
| Remaining individualsnot grpmax-eligible | 0.109% | 919 |
| European (non-Finnish) | 0.00738% | 13,555 |
| South Asian | 0.0022% | 45,438 |
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
- DLGAP1
- Protein
- p.Pro824=
- Coding
- c.2472C>T
- MANE Select
- NM_004746
- dbSNP
- rs73939849
- Type
- single nucleotide variant
- Location
- chr18:3534201 (GRCh38)
- Gene constraint
- LOEUF 0.224 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.85 · 3 PDB
Similar variants
- DLGAP1 p.Ala659= Benign ★★ same type
- DLGAP1 p.Ser296= Benign ★★ same type
- DLGAP1 p.Thr284= Benign ★★ same type
- DLGAP1 p.Thr624= Benign ★★ same type
- DLGAP1 p.Ala173Val Uncertain significance ★ ⚠ same type
- DLGAP1 p.Ala189Thr Uncertain significance ★ ⚠ same type
- DLGAP1 p.Ala302Val Uncertain significance ★ ⚠ same type
- DLGAP1 p.Ala444Ser 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/dlgap1-p-pro824 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown