DLX6 p.Arg111=
c.333C>G · rs749816102 · VCV3050908
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0185%, eas)
Conditions
1
DLX6-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 | GERP 0.36, phastCons 1 |
| Overall | ||
| CADD | 12.43 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0185%
East Asian · 7/37,858 alleles
Filtering AF
0.00865%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00611%
Overall
0.000947%
13/1,372,652 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0185% | 5,408 |
| Remaining individualsnot grpmax-eligible | 0.00508% | 19,677 |
| European (non-Finnish) | 0.000265% | 377,802 |
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
- DLX6
- Protein
- p.Arg111=
- Coding
- c.333C>G
- MANE Select
- NM_005222
- dbSNP
- rs749816102
- Type
- single nucleotide variant
- Location
- chr7:97006310 (GRCh38)
- Gene constraint
- LOEUF 0.379 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.64
- Residue 111
- the 'disordered' region
Disease context
DLX6-related disorder
Similar variants
- DLX6 p.Ala79= Likely benign same condition
- DLX6 p.Ala80= Likely benign same condition
- DLX6 p.Ala81= Likely benign same condition
- DLX6 p.Ala82= Likely benign same condition
- DLX6 p.Gly97= Likely benign same condition
- DLX6 p.Ala82Val Uncertain significance ★★ same type
- DLX6 c.437-85A>C Benign ★★ same type
- DLX6 c.*9A>G 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/dlx6-p-arg111 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown