DLX2 p.Ala297=
c.891G>T · rs149742254 · VCV722902
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.247%, mid)
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 1 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 12.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.247%
Middle Eastern · 14/5,666 alleles
Filtering AF
0.149%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.12%
Overall
0.0389%
608/1,563,614 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.247% | 405 |
| Finnishnot grpmax-eligible | 0.139% | 722 |
| Remaining individualsnot grpmax-eligible | 0.0782% | 1,278 |
| South Asian | 0.057% | 1,754 |
| Admixed American | 0.0476% | 2,100 |
| European (non-Finnish) | 0.0327% | 3,055 |
| African / African-American | 0.00989% | 10,114 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00762% | 13,118 |
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
- DLX2
- Protein
- p.Ala297=
- Coding
- c.891G>T
- MANE Select
- NM_004405
- dbSNP
- rs149742254
- Type
- single nucleotide variant
- Location
- chr2:172100639 (GRCh38)
- Gene constraint
- LOEUF 0.529 · pLI 0.96 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 60.10
Similar variants
- DLX2 p.Ala85= Benign ★★ same type
- DLX2 p.Ala19Ser Uncertain significance ★ ⚠ same type
- DLX2 p.Ala239Thr Uncertain significance ★ ⚠ same type
- DLX2 p.Ala61Thr Uncertain significance ★ ⚠ same type
- DLX2 p.Ala74Val Uncertain significance ★ ⚠ same type
- DLX2 p.Asn99Lys Uncertain significance ★ ⚠ same type
- DLX2 p.Asp63Asn Uncertain significance ★ ⚠ same type
- DLX2 p.Gln247Pro 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/dlx2-p-ala297 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown