DLG3 p.Ser488fs
c.1462dup · VCV3770158
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
intellectual disability, X-linked 90
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 10 of 19 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.9 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- DLG3
- Protein
- p.Ser488fs
- Coding
- c.1462dup
- MANE Select
- NM_021120
- Type
- Duplication
- Location
- chrX:70479205 (GRCh38)
- Structure
- AlphaFold pLDDT 74.35 · 3 PDB
Similar variants
- DLG3 p.Asn45fs Likely pathogenic ★ same condition
- DLG3 p.Ser339fs Likely pathogenic ★ same condition
- DLG3 p.Tyr39Ter Likely pathogenic ★ same condition
- DLG3 c.-8dup Conflicting classifications of pathogenicity ★ same condition
- DLG3 p.Thr365fs Pathogenic same condition
- DLG3 p.Arg217Ter Pathogenic ★★ same condition
- DLG3 p.Arg756Ter Pathogenic ★★ same condition
- DLG3 p.Val459fs 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/dlg3-p-ser488fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown