DLGAP1 p.Ala659=
c.1977T>C · rs61732678 · VCV790190
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.14%, 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 0.28 | GERP 0.33, phastCons 0.39 |
| Overall | ||
| CADD | 6.357 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.14%
African / African-American · 3,105/75,010 alleles
Filtering AF
4.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.97%
Overall
0.212%
3,423/1,613,884 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.14% | 24 |
| Remaining individualsnot grpmax-eligible | 0.237% | 422 |
| Admixed American | 0.218% | 458 |
| Middle Eastern | 0.0825% | 1,212 |
| South Asian | 0.00549% | 18,212 |
| European (non-Finnish) | 0.00246% | 40,686 |
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.Ala659=
- Coding
- c.1977T>C
- MANE Select
- NM_004746
- dbSNP
- rs61732678
- Type
- single nucleotide variant
- Location
- chr18:3567570 (GRCh38)
- Gene constraint
- LOEUF 0.224 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.85 · 3 PDB
- Residue 659
- the 'interaction with dyl2' region
Similar variants
- DLGAP1 p.Pro824= 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-ala659 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown