DLX6 p.Ser16=
c.48G>T · VCV3616840
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0108%, afr)
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 3.7 | GERP -0.16, phastCons 1 |
| Overall | ||
| CADD | 10.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0108%
African / African-American · 8/74,362 alleles
Filtering AF
0.00531%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00383%
Overall
0.000752%
12/1,596,694 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0108% | 9,295 |
| South Asian | 0.00341% | 29,357 |
| European (non-Finnish) | 8.53e-05% | 1,172,387 |
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.Ser16=
- Coding
- c.48G>T
- MANE Select
- NM_005222
- Type
- single nucleotide variant
- Location
- chr7:97006025 (GRCh38)
- Gene constraint
- LOEUF 0.379 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.64
- Residue 16
- the 'disordered' region
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.Ala136Glu 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-ser16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown