DLG4 p.Ala435=
c.1305C>A · rs200879867 · VCV3036143
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00179%, nfe)
Conditions
1
DLG4-related disorder
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 4.5 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 11.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00179%
European (non-Finnish) · 21/1,174,518 alleles
Filtering AF
0.00115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000975%
Overall
0.00131%
21/1,601,864 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
- Protein
- p.Ala435=
- Coding
- c.1305C>A
- MANE Select
- NM_001321075
- dbSNP
- rs200879867
- Type
- single nucleotide variant
- Location
- chr17:7194492 (GRCh38)
- Gene constraint
- LOEUF 0.151 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.00 · 24 PDB
- Residue 435
- a UniProt-annotated variant site (in mrd62); the sh3 domain
Disease context
DLG4-related disorder
Similar variants
- DLG4 c.1543+2T>C Pathogenic/Likely pathogenic ★★ same condition
- DLG4 c.1693+1G>A Pathogenic/Likely pathogenic ★★ same condition
- DLG4 p.Arg309Ter Pathogenic/Likely pathogenic ★★ same condition
- DLG4 p.Arg516Ter Pathogenic ★★ same condition
- DLG4 p.Arg586Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- DLG4 p.Arg617Ter Pathogenic ★★ same condition
- DLG4 c.1515+1G>A Likely pathogenic ★ same condition
- DLG4 c.1694-2A>G Likely 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-p-ala435 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown