DLGAP4 p.Asn607=
c.1821C>T · rs146720610 · VCV736679
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0659%, sas)
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 1.1 | GERP -0.64, phastCons 1 |
| Overall | ||
| CADD | 10.81 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0659%
South Asian · 60/91,084 alleles
Filtering AF
0.0542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0528%
Overall
0.0488%
788/1,614,236 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0659% | 1,518 |
| European (non-Finnish) | 0.0579% | 1,728 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| Finnishnot grpmax-eligible | 0.00937% | 10,674 |
| African / African-American | 0.00799% | 12,508 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,803 |
| Admixed American | 0.00666% | 15,008 |
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
- DLGAP4
- Protein
- p.Asn607=
- Coding
- c.1821C>T
- MANE Select
- NM_001365621
- dbSNP
- rs146720610
- Type
- single nucleotide variant
- Location
- chr20:36496877 (GRCh38)
- Gene constraint
- LOEUF 0.331 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.01
- Residue 607
- the 'disordered' region
Similar variants
- DLGAP4 p.Pro572Leu Uncertain significance ★★ ⚠ same type
- DLGAP4 p.Ala845= Benign ★★ same type
- DLGAP4 p.Gly540Ser Likely benign ★★ same type
- DLGAP4 p.Pro270= Likely benign ★★ same type
- DLGAP4 c.2011-343A>T Uncertain significance ★ same type
- DLGAP4 p.Ala131Thr Uncertain significance ★ ⚠ same type
- DLGAP4 p.Ala154Pro Uncertain significance ★ ⚠ same type
- DLGAP4 p.Ala154Ser 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/dlgap4-p-asn607 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown