DLGAP3 p.Ala347=
c.1041C>T · rs754381123 · VCV756641
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -3 | GERP -3.7 |
| Overall | ||
| CADD | 2.295 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.0117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0111%
Overall
0.0104%
167/1,612,006 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| European (non-Finnish) | 0.0135% | 7,422 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| East Asian | 0.00223% | 44,890 |
| Admixed American | 0.00167% | 59,998 |
| African / African-American | 0.00133% | 74,954 |
| South Asian | 0.0011% | 91,094 |
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
- DLGAP3
- Protein
- p.Ala347=
- Coding
- c.1041C>T
- MANE Select
- NM_001080418
- dbSNP
- rs754381123
- Type
- single nucleotide variant
- Location
- chr1:34904343 (GRCh38)
- Gene constraint
- LOEUF 0.367 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.83
Similar variants
- DLGAP3 p.Arg793= Benign ★★ same type
- DLGAP3 p.Gly306= Benign ★★ same type
- DLGAP3 p.Pro764= Benign ★★ same type
- DLGAP3 p.Ser406= Benign/Likely benign ★★ same type
- DLGAP3 p.Thr334= Benign ★★ same type
- DLGAP3 p.Lys889Arg Uncertain significance ★ ⚠ same type
- DLGAP3 p.Arg627= Benign ★ same type
- DLGAP3 p.Pro45His 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/dlgap3-p-ala347 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown