DLG4 c.1869dupG
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 9.23e-05%, nfe)
Conditions
1
intellectual developmental disorder 62
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2.4, phastCons 1 |
| Non-coding constraint | Z 6.64 | 1 kb window · o/e 0.60 · regional · uncalibrated |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.23e-05%
European (non-Finnish) · 1/1,083,692 alleles
Overall
7.84e-05%
1/1,275,936 alleles · very rare
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
- DLG4
- Coding
- c.1869dupG
- MANE Select
- NM_001321075
- Type
- Duplication
- Location
- chr17:7191999 (GRCh38)
- Gene constraint
- LOEUF 0.151 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.00 · 24 PDB
Similar variants
- DLG4 p.Asp479Ter Pathogenic/Likely pathogenic ★★ same condition
- DLG4 p.Gly176fs Pathogenic ★★ same condition
- DLG4 p.Gly82fs Pathogenic ★★ same condition
- DLG4 p.Tyr50fs Pathogenic/Likely pathogenic ★★ same condition
- DLG4 p.Asn326fs Pathogenic ★ same condition
- DLG4 p.Asp695Ter Pathogenic ★ same condition
- DLG4 p.Glu524fs Likely pathogenic ★ same condition
- DLG4 p.Gly49fs Pathogenic ★ same condition
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/dlg4-c-1869dupg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown