DLGAP1 p.His749=
c.2247T>C · rs140250387 · VCV727983
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.17%, 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 -1.9 | GERP -3.4 |
| Overall | ||
| CADD | 1.003 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.17%
European (non-Finnish) · 2,009/1,180,034 alleles
Filtering AF
0.164%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.162%
Overall
0.131%
2,108/1,614,056 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.17% | 587 |
| Remaining individualsnot grpmax-eligible | 0.072% | 1,389 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0338% | 2,961 |
| African / African-American | 0.028% | 3,568 |
| Middle Eastern | 0.0164% | 6,084 |
| Finnishnot grpmax-eligible | 0.0125% | 8,004 |
| Admixed American | 0.0117% | 8,573 |
| South Asian | 0.00769% | 13,012 |
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
- DLGAP1
- Protein
- p.His749=
- Coding
- c.2247T>C
- MANE Select
- NM_004746
- dbSNP
- rs140250387
- Type
- single nucleotide variant
- Location
- chr18:3534426 (GRCh38)
- Gene constraint
- LOEUF 0.224 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.85 · 3 PDB
Similar variants
- DLGAP1 p.Ala659= Benign ★★ same type
- DLGAP1 p.Pro824= Benign ★★ same type
- DLGAP1 p.Ser296= Benign ★★ same type
- DLGAP1 p.Thr284= Benign ★★ same type
- DLGAP1 p.Thr624= Benign ★★ same type
- DLGAP1 p.Ala173Val Uncertain significance ★ ⚠ same type
- DLGAP1 p.Ala189Thr Uncertain significance ★ ⚠ same type
- DLGAP1 p.Ala302Val 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/dlgap1-p-his749 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown