DLG2 p.Ser499=
c.1497T>C · VCV3502328
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0249%, eas)
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 8 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 15.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0249%
East Asian · 11/44,186 alleles
Filtering AF
0.0139%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0107%
Overall
0.000833%
12/1,441,310 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0249% | 4,017 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,438 |
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
- DLG2
- Protein
- p.Ser499=
- Coding
- c.1497T>C
- MANE Select
- NM_001142699
- Type
- single nucleotide variant
- Location
- chr11:83874488 (GRCh38)
- Gene constraint
- LOEUF 0.444 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.93 · 2 PDB
- Residue 499
- the pdz 3 domain; a β-strand
Similar variants
- DLG2 p.Arg797= Benign ★★ same type
- DLG2 p.Gln944= Benign ★★ same type
- DLG2 p.Leu459= Benign ★★ same type
- DLG2 p.Leu514Pro Likely benign ★★ same type
- DLG2 p.Lys59= Benign ★★ same type
- DLG2 p.Ser804= Benign/Likely benign ★★ same type
- DLG2 c.624+1G>A Uncertain significance ★ same type
- DLG2 p.Ala128Pro 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/dlg2-p-ser499 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown