DLX4 p.Pro145=
c.435C>T · rs769369952 · VCV3054114
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0141%, nfe)
Conditions
1
DLX4-related disorder
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 -2.8 | GERP -1.4 |
| Overall | ||
| CADD | 9.314 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0141%
European (non-Finnish) · 166/1,180,044 alleles
Filtering AF
0.0123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0116%
Overall
0.0106%
171/1,614,012 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0141% | 7,109 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,830 |
| African / African-American | 0.00267% | 37,468 |
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
- DLX4
- Protein
- p.Pro145=
- Coding
- c.435C>T
- MANE Select
- NM_138281
- dbSNP
- rs769369952
- Type
- single nucleotide variant
- Location
- chr17:49973224 (GRCh38)
- Gene constraint
- LOEUF 1.056 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.80
- Residue 145
- a DNA-binding region
Disease context
DLX4-related disorder
Similar variants
- DLX4 p.Pro110Ser Uncertain significance ⚠ same condition
- DLX4 c.284-31G>A Likely benign same condition
- DLX4 p.Ala77= Likely benign same condition
- DLX4 p.Arg169= Likely benign same condition
- DLX4 p.Leu154= Likely benign same condition
- DLX4 p.Pro25Arg Likely benign ⚠ same condition
- DLX4 p.Ala77Thr Uncertain significance ★★ ⚠ same type
- DLX4 p.Leu201His 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/dlx4-p-pro145 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown