DLX5 p.Ser232=
c.696G>C · rs371372992 · VCV3039274
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.435%, sas)
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 -5.4 | GERP -3.1 |
| Overall | ||
| CADD | 3.618 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.435%
South Asian · 396/91,062 alleles
Filtering AF
0.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.386%
Overall
0.0265%
428/1,614,080 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.435% | 230 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,232 |
| Middle Eastern | 0.0167% | 5,992 |
| African / African-American | 0.004% | 25,023 |
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.Ser232=
- Coding
- c.696G>C
- MANE Select
- NM_005221
- dbSNP
- rs371372992
- Type
- single nucleotide variant
- Location
- chr7:97020910 (GRCh38)
- Gene constraint
- LOEUF 0.498 · pLI 0.98 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.56 · 2 PDB
- Residue 232
- the 'disordered' region
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-ser232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown