LMX1B p.Pro124=
c.372C>T · rs374078636 · VCV1895915
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00195%, nfe)
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 0.33 | GERP -0.051, phastCons 0.99 |
| Overall | ||
| CADD | 11.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00195%
European (non-Finnish) · 23/1,179,964 alleles
Filtering AF
0.0013%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00108%
Overall
0.00143%
23/1,613,592 alleles · very rare
exomes 21/1,461,356 · genomes 2/152,236 · joint denominator
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
- LMX1B
- Protein
- p.Pro124=
- Coding
- c.372C>T
- MANE Select
- NM_001174147
- dbSNP
- rs374078636
- Type
- single nucleotide variant
- Location
- chr9:126690881 (GRCh38)
- Gene constraint
- LOEUF 0.409 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 70.79
- Residue 124
- the lim zinc-binding 2 domain
Similar variants
- LMX1B c.741+1G>A Pathogenic ★★ same type
- LMX1B c.819+1G>A Pathogenic ★★ same type
- LMX1B p.Ala236Pro Pathogenic ★★ same type
- LMX1B p.Arg221Ter Pathogenic ★★ same type
- LMX1B p.Arg223Gln Pathogenic ★★ same type
- LMX1B p.Arg223Trp Pathogenic/Likely pathogenic ★★ same type
- LMX1B p.Arg231Ter Pathogenic/Likely pathogenic ★★ same type
- LMX1B p.Arg246Gln Pathogenic ★★ 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/lmx1b-p-pro124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown