DLG5 p.Pro1048=
c.3144G>A · rs74820799 · VCV786781
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.24%, 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 -14 | |
| Overall | ||
| CADD | 0.039 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.24%
East Asian · 557/44,862 alleles
Filtering AF
1.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.12%
Overall
0.102%
1,650/1,612,940 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.24% | 81 |
| Admixed American | 0.868% | 115 |
| South Asian | 0.164% | 611 |
| Remaining individualsnot grpmax-eligible | 0.126% | 791 |
| Finnishnot grpmax-eligible | 0.0937% | 1,067 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0743% | 1,346 |
| Middle Eastern | 0.0495% | 2,020 |
| European (non-Finnish) | 0.0211% | 4,739 |
| African / African-American | 0.0147% | 6,818 |
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.Pro1048=
- Coding
- c.3144G>A
- MANE Select
- NM_004747
- dbSNP
- rs74820799
- Type
- single nucleotide variant
- Location
- chr10:77821340 (GRCh38)
- Gene constraint
- LOEUF 0.333 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.25 · 1 PDB
- Residue 1048
- a UniProt-annotated variant site (in yuvob; likely pathogenic; fails to fully rescue abnormal pronephros development and ventriculomegaly when expressed in dlg5-null xenopus embryos); the 'disordered' region
Similar variants
- DLG5 p.Pro1048Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro1048 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown