DLGAP4 p.Ala845=
c.2535T>C · rs35338208 · VCV769088
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 8.44%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.98 | GERP -4.4, phastCons 0.005 |
| Overall | ||
| CADD | 5.166 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.44%
African / African-American · 6,334/75,056 alleles
Filtering AF
8.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.19%
Overall
0.441%
7,120/1,614,218 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.44% | 12 |
| Remaining individualsnot grpmax-eligible | 0.514% | 195 |
| Admixed American | 0.483% | 207 |
| Middle Eastern | 0.346% | 289 |
| South Asian | 0.0209% | 4,794 |
| European (non-Finnish) | 0.0114% | 8,741 |
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
- DLGAP4
- Protein
- p.Ala845=
- Coding
- c.2535T>C
- MANE Select
- NM_001365621
- dbSNP
- rs35338208
- Type
- single nucleotide variant
- Location
- chr20:36524272 (GRCh38)
- Gene constraint
- LOEUF 0.331 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.01
Similar variants
- DLGAP4 p.Pro572Leu Uncertain significance ★★ ⚠ same type
- DLGAP4 p.Gly540Ser Likely benign ★★ same type
- DLGAP4 p.Pro270= Likely benign ★★ same type
- DLGAP4 c.2011-343A>T Uncertain significance ★ same type
- DLGAP4 p.Ala131Thr Uncertain significance ★ ⚠ same type
- DLGAP4 p.Ala154Pro Uncertain significance ★ ⚠ same type
- DLGAP4 p.Ala154Ser Uncertain significance ★ ⚠ same type
- DLGAP4 p.Ala161Val 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/dlgap4-p-ala845 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown