DLGAP3 p.Arg627=
c.1881G>A · rs113637749 · VCV739639
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.336%, 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 0.57 | GERP -5.3, phastCons 1 |
| Overall | ||
| CADD | 9.791 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.336%
African / African-American · 252/75,066 alleles
Filtering AF
0.302%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.288%
Overall
0.0194%
312/1,609,154 alleles · rare
exomes 191/1,456,772 · genomes 121/152,382 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.336% | 298 |
| Remaining individualsnot grpmax-eligible | 0.0785% | 1,275 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.01% | 10,003 |
| European (non-Finnish) | 0.000339% | 294,966 |
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.Arg627=
- Coding
- c.1881G>A
- MANE Select
- NM_001080418
- dbSNP
- rs113637749
- Type
- single nucleotide variant
- Location
- chr1:34885511 (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.Ala347= Likely 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-arg627 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown