DLX5 p.Ile183=
c.549C>T · rs1049250299 · VCV2079506
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00836%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.40 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP -0.91, phastCons 1 |
| Overall | ||
| CADD | 17.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00836%
Admixed American · 5/59,774 alleles
Filtering AF
0.00324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.000499%
8/1,603,310 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00836% | 11,955 |
| Remaining individualsnot grpmax-eligible | 0.00485% | 20,618 |
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.Ile183=
- Coding
- c.549C>T
- MANE Select
- NM_005221
- dbSNP
- rs1049250299
- Type
- single nucleotide variant
- Location
- chr7:97021057 (GRCh38)
- Gene constraint
- LOEUF 0.498 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.56 · 2 PDB
- Residue 183
- a DNA-binding region; an α-helix
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-ile183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown