DLG4 p.Val658=
c.1974G>A · rs759932966 · VCV737883
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.104%, amr)
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 0.38 | GERP -4.5, phastCons 0.99 |
| Overall | ||
| CADD | 11.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.104%
Admixed American · 42/40,450 alleles
Filtering AF
0.0789%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0702%
Overall
0.00294%
43/1,464,040 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.104% | 963 |
| Remaining individualsnot grpmax-eligible | 0.0018% | 55,404 |
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.Val658=
- Coding
- c.1974G>A
- MANE Select
- NM_001321075
- dbSNP
- rs759932966
- Type
- single nucleotide variant
- Location
- chr17:7191895 (GRCh38)
- Gene constraint
- LOEUF 0.151 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.00 · 24 PDB
- Residue 658
- a UniProt-annotated variant site (in mrd62); the guanylate kinase-like domain
Similar variants
- DLG4 c.1084-1G>T Pathogenic/Likely pathogenic ★★ same type
- DLG4 c.1478+2T>C Pathogenic/Likely pathogenic ★★ same type
- DLG4 c.1543+2T>C Pathogenic/Likely pathogenic ★★ same type
- DLG4 c.1592-1G>A Pathogenic/Likely pathogenic ★★ same type
- DLG4 c.1693+1G>A Pathogenic/Likely pathogenic ★★ same type
- DLG4 c.1866+2T>C Pathogenic/Likely pathogenic ★★ same type
- DLG4 c.210+1G>T Likely pathogenic ★★ same type
- DLG4 c.211-2A>G Pathogenic/Likely pathogenic ★★ 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/dlg4-p-val658 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown