DLX3 p.Ser84=
c.252G>A · rs139226711 · VCV324025
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0603%, 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 3.4 | GERP -0.33, phastCons 1 |
| Overall | ||
| CADD | 15.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0603%
European (non-Finnish) · 711/1,180,052 alleles
Filtering AF
0.0565%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0551%
Overall
0.0465%
751/1,614,078 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0603% | 1,660 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,471 |
| African / African-American | 0.02% | 4,996 |
| Admixed American | 0.005% | 20,001 |
| Finnishnot grpmax-eligible | 0.00469% | 21,343 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
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
- DLX3
- Protein
- p.Ser84=
- Coding
- c.252G>A
- MANE Select
- NM_005220
- dbSNP
- rs139226711
- Type
- single nucleotide variant
- Location
- chr17:49994747 (GRCh38)
- Gene constraint
- LOEUF 0.559 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 60.87 · 1 PDB
Similar variants
- DLX3 p.Gln178His Pathogenic/Likely pathogenic ★★ same type
- DLX3 p.Ala214Thr Uncertain significance ★★ ⚠ same type
- DLX3 p.Ala45Pro Uncertain significance ★★ ⚠ same type
- DLX3 p.Arg146Cys Uncertain significance ★★ ⚠ same type
- DLX3 p.Arg228Cys Uncertain significance ★★ ⚠ same type
- DLX3 p.Arg7Gly Uncertain significance ★★ same type
- DLX3 p.Asn200Ser Uncertain significance ★★ ⚠ same type
- DLX3 p.Asn282Lys 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/dlx3-p-ser84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown