DLX6 p.Ala136Glu
c.407C>A · rs1399051213 · VCV2292433
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000277%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.29 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.1 | GERP -3.4, phastCons 1 |
| Regional constraint | o/e 1.24 | unconstrained · MANE · 1,662 bp · p 0.00049 · regional, not allelic |
| Overall | ||
| CADD | 22.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000277%
European (non-Finnish) · 3/1,084,184 alleles
Filtering AF
7.4e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2e-05%
Overall
0.000209%
3/1,437,442 alleles · very rare
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.Ala136Glu
- Coding
- c.407C>A
- MANE Select
- NM_005222
- dbSNP
- rs1399051213
- Type
- single nucleotide variant
- Location
- chr7:97006384 (GRCh38)
- Gene constraint
- LOEUF 0.379 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.64
Similar variants
- DLX6 p.Ala82Val Uncertain significance ★★ same type
- DLX6 c.437-85A>C Benign ★★ same type
- DLX6 c.*9A>G Benign ★★ same type
- DLX6 p.Gln178= Benign ★★ same type
- DLX6 p.Gln35= Likely benign ★★ same type
- DLX6 p.Gln41= Likely benign ★★ same type
- DLX6 p.Pro282= Likely benign ★★ same type
- DLX6 p.Ala250Thr 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-ala136glu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown