DLG2 p.Ser804=
c.2412T>C · rs146333277 · VCV771749
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.348%, nfe)
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 0.52 | GERP -4.1, phastCons 0.87 |
| Overall | ||
| CADD | 7.552 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.348%
European (non-Finnish) · 4,104/1,179,404 alleles
Filtering AF
0.339%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.335%
Overall
0.281%
4,534/1,613,236 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.348% | 287 |
| Ashkenazi Jewishnot grpmax-eligible | 0.331% | 302 |
| Remaining individualsnot grpmax-eligible | 0.213% | 470 |
| Finnishnot grpmax-eligible | 0.17% | 587 |
| Admixed American | 0.0801% | 1,248 |
| African / African-American | 0.0493% | 2,026 |
| Middle Eastern | 0.0165% | 6,058 |
| South Asian | 0.00439% | 22,762 |
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.Ser804=
- Coding
- c.2412T>C
- MANE Select
- NM_001142699
- dbSNP
- rs146333277
- Type
- single nucleotide variant
- Location
- chr11:83471660 (GRCh38)
- Gene constraint
- LOEUF 0.444 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.93 · 2 PDB
- Residue 804
- the guanylate kinase-like domain
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 c.624+1G>A Uncertain significance ★ same type
- DLG2 p.Ala128Pro Uncertain significance ★ ⚠ same type
- DLG2 p.Ala366Thr 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-ser804 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown