DLG3 p.Ser475=
c.1425G>A · rs138204352 · VCV82252
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0857%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.20 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.21 | GERP -3.7, phastCons 0.92 |
| Overall | ||
| CADD | 3.298 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0857%
African / African-American · 49/57,196 alleles
Filtering AF
0.0665%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0598%
Overall
0.0048%
58/1,207,586 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0857% | 1,167 |
| Admixed American | 0.00874% | 11,446 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,538 |
| European (non-Finnish) | 0.000448% | 223,240 |
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
- DLG3
- Protein
- p.Ser475=
- Coding
- c.1425G>A
- MANE Select
- NM_021120
- dbSNP
- rs138204352
- Type
- single nucleotide variant
- Location
- chrX:70479169 (GRCh38)
- Structure
- AlphaFold pLDDT 74.35 · 3 PDB
- Residue 475
- an α-helix
Similar variants
- DLG3 p.Ser475Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- DLG3 p.Arg211Ter Pathogenic ★★ same type
- DLG3 p.Arg217Ter Pathogenic ★★ same type
- DLG3 p.Arg679Ter Pathogenic/Likely pathogenic ★★ same type
- DLG3 p.Arg756Ter Pathogenic ★★ same type
- DLG3 p.Ala627Ser Uncertain significance ★★ ⚠ same type
- DLG3 p.Arg217Gln Uncertain significance ★★ ⚠ same type
- DLG3 p.Arg271Cys 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/dlg3-p-ser475 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown