DLG5 p.Ile279=
c.837C>T · VCV4823052
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00348%, 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 -6.3 | |
| Overall | ||
| CADD | 1.258 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00348%
Admixed American · 2/57,542 alleles
Filtering AF
0.000576%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000216%
Overall
0.000696%
10/1,436,068 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00348% | 28,771 |
| African / African-American | 0.00134% | 74,726 |
| European (non-Finnish) | 0.000601% | 166,428 |
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
- DLG5
- Protein
- p.Ile279=
- Coding
- c.837C>T
- MANE Select
- NM_004747
- Type
- single nucleotide variant
- Location
- chr10:77853381 (GRCh38)
- Gene constraint
- LOEUF 0.333 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.25 · 1 PDB
Similar variants
- DLG5 p.Arg166Cys Uncertain significance ★★ ⚠ same type
- DLG5 p.Leu1192Pro Uncertain significance ★★ ⚠ same type
- DLG5 c.1622+8G>A Benign ★★ same type
- DLG5 c.3672-5C>T Benign/Likely benign ★★ same type
- DLG5 p.Ala1447= Benign ★★ same type
- DLG5 p.Ala1600Val Benign ★★ same type
- DLG5 p.Ala1738Thr Benign ★★ same type
- DLG5 p.Ala741= Benign/Likely benign ★★ 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/dlg5-p-ile279 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown