DLG2 p.Ala583=
c.1749A>T · rs35062128 · VCV789630
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.31%, afr)
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 -1.3 | GERP -3.7, phastCons 0.001 |
| Overall | ||
| CADD | 6.015 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.31%
African / African-American · 2,482/75,032 alleles
Filtering AF
3.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.16%
Overall
0.171%
2,766/1,614,122 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.31% | 30 |
| Remaining individualsnot grpmax-eligible | 0.21% | 477 |
| Admixed American | 0.177% | 566 |
| Middle Eastern | 0.099% | 1,010 |
| European (non-Finnish) | 0.00339% | 29,500 |
| South Asian | 0.0011% | 91,082 |
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
- DLG2
- Protein
- p.Ala583=
- Coding
- c.1749A>T
- MANE Select
- NM_001142699
- dbSNP
- rs35062128
- Type
- single nucleotide variant
- Location
- chr11:83786766 (GRCh38)
- Gene constraint
- LOEUF 0.444 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.93 · 2 PDB
- Residue 583
- the sh3 domain
Similar variants
- DLG2 p.Ala583Val Uncertain significance ★ ⚠ same residue
- DLG2 p.Arg797= Benign ★★ same type
- DLG2 p.Gln944= Benign ★★ same type
- DLG2 p.Leu459= Benign ★★ same type
- DLG2 p.Leu514Pro Likely benign ★★ same type
- DLG2 p.Lys59= Benign ★★ same type
- DLG2 p.Ser804= Benign/Likely benign ★★ same type
- DLG2 c.624+1G>A Uncertain significance ★ 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/dlg2-p-ala583 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown