DLG4 p.Pro153=
c.459C>T · rs370864740 · VCV734483
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.223%, sas)
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 -0.2 | GERP -4.8, phastCons 0.029 |
| Overall | ||
| CADD | 4.976 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.223%
South Asian · 203/91,046 alleles
Filtering AF
0.198%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.188%
Overall
0.0288%
464/1,612,606 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.223% | 449 |
| Middle Eastern | 0.0495% | 2,019 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,901 |
| European (non-Finnish) | 0.0201% | 4,974 |
| Admixed American | 0.005% | 19,999 |
| Finnishnot grpmax-eligible | 0.00313% | 31,989 |
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.Pro153=
- Coding
- c.459C>T
- MANE Select
- NM_001321075
- dbSNP
- rs370864740
- Type
- single nucleotide variant
- Location
- chr17:7203470 (GRCh38)
- Gene constraint
- LOEUF 0.151 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 78.00 · 24 PDB
- Residue 153
- an α-helix
Similar variants
- DLG4 p.Pro153Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown