LBX1 p.Pro238=
c.714C>G · rs200155323 · VCV780888
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.85%, 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 0.77 | GERP -1.3, phastCons 1 |
| Overall | ||
| CADD | 2.224 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.85%
African / African-American · 2,124/74,538 alleles
Filtering AF
2.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.71%
Overall
0.167%
2,677/1,601,648 alleles · low-frequency
exomes 1,426/1,449,314 · genomes 1,251/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.85% | 35 |
| Admixed American | 0.259% | 386 |
| Remaining individualsnot grpmax-eligible | 0.168% | 595 |
| Ashkenazi Jewishnot grpmax-eligible | 0.126% | 792 |
| Middle Eastern | 0.0993% | 1,007 |
| European (non-Finnish) | 0.0211% | 4,744 |
| Finnishnot grpmax-eligible | 0.00504% | 19,831 |
| South Asian | 0.00332% | 30,150 |
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
- LBX1
- Protein
- p.Pro238=
- Coding
- c.714C>G
- MANE Select
- NM_006562
- dbSNP
- rs200155323
- Type
- single nucleotide variant
- Location
- chr10:101227402 (GRCh38)
- Gene constraint
- LOEUF 0.753 · pLI 0.45 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.61
- Residue 238
- the 'disordered' region
Similar variants
- LBX1 p.Pro238His Uncertain significance ★ ⚠ same residue
- LBX1 p.Arg76= Benign ★★ same type
- LBX1 p.Ala107Val Uncertain significance ★ ⚠ same type
- LBX1 p.Ala228Pro Uncertain significance ★ ⚠ same type
- LBX1 p.Ala241Asp Uncertain significance ★ ⚠ same type
- LBX1 p.Ala241Ser Uncertain significance ★ ⚠ same type
- LBX1 p.Ala56Ser Uncertain significance ★ ⚠ same type
- LBX1 p.Ala67Thr 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/lbx1-p-pro238 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown