DLGAP3 p.Pro764=
c.2292C>T · rs201441073 · VCV786723
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.23%, 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 -8.7 | GERP -5.5 |
| Overall | ||
| CADD | 0.921 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.23%
African / African-American · 1,660/74,596 alleles
Filtering AF
2.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.1%
Overall
0.128%
2,021/1,582,906 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.23% | 45 |
| Remaining individualsnot grpmax-eligible | 0.177% | 564 |
| Middle Eastern | 0.153% | 652 |
| Ashkenazi Jewishnot grpmax-eligible | 0.131% | 763 |
| Admixed American | 0.126% | 791 |
| South Asian | 0.0112% | 8,934 |
| European (non-Finnish) | 0.0103% | 9,741 |
| East Asian | 0.00226% | 44,210 |
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
- DLGAP3
- Protein
- p.Pro764=
- Coding
- c.2292C>T
- MANE Select
- NM_001080418
- dbSNP
- rs201441073
- Type
- single nucleotide variant
- Location
- chr1:34868798 (GRCh38)
- Gene constraint
- LOEUF 0.367 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.83
- Residue 764
- the 'disordered' region
Similar variants
- DLGAP3 p.Arg793= Benign ★★ same type
- DLGAP3 p.Gly306= Benign ★★ same type
- DLGAP3 p.Ser406= Benign/Likely benign ★★ same type
- DLGAP3 p.Thr334= Benign ★★ same type
- DLGAP3 p.Lys889Arg Uncertain significance ★ ⚠ same type
- DLGAP3 p.Ala347= Likely benign ★ same type
- DLGAP3 p.Arg627= Benign ★ same type
- DLGAP3 p.Pro45His 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/dlgap3-p-pro764 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown