DLX6 p.Pro53del
c.134CGC[8] · rs559903070 · VCV1600917
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.278%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.84 | GERP -2.3, phastCons 0.12 |
| Overall | ||
| CADD | 11.31 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (GCA)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.278%
Admixed American · 127/45,610 alleles
Filtering AF
0.255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.252%
Overall
0.253%
3,629/1,436,886 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.278% | 359 |
| European (non-Finnish) | 0.263% | 380 |
| African / African-American | 0.254% | 393 |
| South Asian | 0.224% | 447 |
| Remaining individualsnot grpmax-eligible | 0.212% | 472 |
| East Asian | 0.201% | 499 |
| Finnishnot grpmax-eligible | 0.185% | 540 |
| Ashkenazi Jewishnot grpmax-eligible | 0.168% | 596 |
| Middle Eastern | 0.126% | 791 |
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.Pro53del
- Coding
- c.134CGC[8]
- MANE Select
- NM_005222
- dbSNP
- rs559903070
- Type
- Microsatellite
- Location
- chr7:97006109 (GRCh38)
- Gene constraint
- LOEUF 0.379 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.64
- Residue 53
- a DNA-binding region
Similar variants
- DLX6 p.Pro53dup Benign ★★ same residue
- DLX6 p.Pro53_Gln54insProProProPro Uncertain significance ★ same residue
- DLX6 p.Pro51_Pro53del Benign ★★ same type
- DLX6 p.Ala83_Gly84insAlaAla Uncertain significance ★ same type
- DLX6 p.Gln37_Gln44del Uncertain significance ★ same type
- DLX6 p.Gln37_Gln44dup Conflicting classifications of pathogenicity ★ same type
- DLX6 p.Gln41_Gln44del Uncertain significance ★ same type
- DLX6 p.Gln42_Gln44del 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/dlx6-p-pro53del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown