DLX5 p.Val223=
c.669G>T · rs763057428 · VCV2991335
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
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 2.7 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 8.912 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/60,016 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.000496%
8/1,613,956 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,574 |
| European (non-Finnish) | 8.47e-05% | 1,180,057 |
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
- DLX5
- Protein
- p.Val223=
- Coding
- c.669G>T
- MANE Select
- NM_005221
- dbSNP
- rs763057428
- Type
- single nucleotide variant
- Location
- chr7:97020937 (GRCh38)
- Gene constraint
- LOEUF 0.498 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.56 · 2 PDB
- Residue 223
- the 'disordered' region
Similar variants
- DLX5 p.Asp44Tyr Uncertain significance ★★ ⚠ same type
- DLX5 p.Asp46Glu Uncertain significance ★★ ⚠ same type
- DLX5 p.His238Asn Uncertain significance ★★ ⚠ same type
- DLX5 p.His279Tyr Uncertain significance ★★ ⚠ same type
- DLX5 p.Pro30Leu Uncertain significance ★★ ⚠ same type
- DLX5 p.Ser229Pro Uncertain significance ★★ ⚠ same type
- DLX5 p.Tyr108Cys Uncertain significance ★★ ⚠ same type
- DLX5 c.540+227C>T 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/dlx5-p-val223 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown