DLG3 p.Val16=
c.48G>C · rs1271952490 · VCV1743971
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00771%, amr)
Conditions
1
Inborn genetic diseases
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 8.2 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 12.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00771%
Admixed American · 3/38,924 alleles
Filtering AF
0.00204%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00107%
Overall
0.000286%
3/1,050,140 alleles · very rare
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
- DLG3
- Protein
- p.Val16=
- Coding
- c.48G>C
- MANE Select
- NM_021120
- dbSNP
- rs1271952490
- Type
- single nucleotide variant
- Location
- chrX:70445249 (GRCh38)
- Structure
- AlphaFold pLDDT 74.35 · 3 PDB
Similar variants
- DLG3 p.Arg211Ter Pathogenic ★★ same condition
- DLG3 p.Arg217Gln Uncertain significance ★★ ⚠ same condition
- DLG3 p.Arg271Cys Uncertain significance ★★ ⚠ same condition
- DLG3 p.Arg497Gln Uncertain significance ★★ ⚠ same condition
- DLG3 p.Arg710Gln Uncertain significance ★★ ⚠ same condition
- DLG3 p.Asp599Asn Uncertain significance ★★ ⚠ same condition
- DLG3 p.Glu222Lys Uncertain significance ★★ ⚠ same condition
- DLG3 p.His2Pro Uncertain significance ★★ ⚠ same condition
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/dlg3-p-val16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown