DLGAP2 p.Pro940=
c.2820G>A · rs777312874 · VCV2658294
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.015 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -6.3 | GERP -4.4 |
| Overall | ||
| CADD | 0.263 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,042 alleles
Filtering AF
0.00726%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00552%
Overall
0.00212%
34/1,600,572 alleles · ultra-rare
exomes 28/1,448,352 · genomes 6/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,042 |
| African / African-American | 0.0134% | 7,458 |
| Finnishnot grpmax-eligible | 0.00793% | 12,606 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,852 |
| Admixed American | 0.0017% | 58,692 |
| European (non-Finnish) | 0.00119% | 83,725 |
| South Asian | 0.00111% | 89,966 |
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
- DLGAP2
- Protein
- p.Pro940=
- Coding
- c.2820G>A
- MANE Select
- NM_001346810
- dbSNP
- rs777312874
- Type
- single nucleotide variant
- Location
- chr8:1697170 (GRCh38)
- Gene constraint
- LOEUF 0.425 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 48.83
Similar variants
- DLGAP2 c.1810+14A>G Benign ★★ same type
- DLGAP2 c.2160+19C>G Benign ★★ same type
- DLGAP2 p.Glu678= Benign ★★ same type
- DLGAP2 p.Pro464Gln Benign ★★ same type
- DLGAP2 c.2203-7G>T Uncertain significance ★ same type
- DLGAP2 p.Ala1019Gly Uncertain significance ★ ⚠ same type
- DLGAP2 p.Ala1026Val Uncertain significance ★ same type
- DLGAP2 p.Ala116Thr 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/dlgap2-p-pro940 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown