DLGAP4 p.Pro270=
c.810G>A · rs763627689 · VCV747057
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.42%, mid)
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 -3.9 | GERP -5.4 |
| Overall | ||
| CADD | 0.206 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.42%
Middle Eastern · 14/3,336 alleles
Filtering AF
0.254%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.203%
Overall
0.00589%
42/712,690 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.42% | 238 |
| Admixed American | 0.0237% | 4,225 |
| Remaining individualsnot grpmax-eligible | 0.0156% | 6,413 |
| European (non-Finnish) | 0.0028% | 35,757 |
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.Pro270=
- Coding
- c.810G>A
- MANE Select
- NM_001365621
- dbSNP
- rs763627689
- Type
- single nucleotide variant
- Location
- chr20:36432527 (GRCh38)
- Gene constraint
- LOEUF 0.331 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.01
Similar variants
- DLGAP4 p.Pro270Leu Uncertain significance ★ ⚠ same residue
- DLGAP4 p.Pro572Leu Uncertain significance ★★ ⚠ same type
- DLGAP4 p.Ala845= Benign ★★ same type
- DLGAP4 p.Gly540Ser 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
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-pro270 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown