DLG5 p.Pro997=
c.2991T>G · rs144503327 · VCV790275
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.627%, 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 1.7 | phastCons 0.47 |
| Overall | ||
| CADD | 6.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.627%
European (non-Finnish) · 7,403/1,179,960 alleles
Filtering AF
0.615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.611%
Overall
0.538%
8,677/1,612,594 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.627% | 159 |
| Finnishnot grpmax-eligible | 0.541% | 185 |
| Remaining individualsnot grpmax-eligible | 0.506% | 198 |
| Middle Eastern | 0.413% | 242 |
| South Asian | 0.4% | 250 |
| Admixed American | 0.262% | 382 |
| African / African-American | 0.0855% | 1,170 |
| Ashkenazi Jewishnot grpmax-eligible | 0.027% | 3,701 |
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.Pro997=
- Coding
- c.2991T>G
- MANE Select
- NM_004747
- dbSNP
- rs144503327
- Type
- single nucleotide variant
- Location
- chr10:77821493 (GRCh38)
- Gene constraint
- LOEUF 0.333 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.25 · 1 PDB
- Residue 997
- 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.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-pro997 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown