LMF1 p.Pro25=
c.75G>C · rs2548412101 · VCV1952226
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00175%, amr)
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 -3.3 | GERP -1.8 |
| Overall | ||
| CADD | 3.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00175%
Admixed American · 1/57,300 alleles
Overall
6.32e-05%
1/1,581,238 alleles · very rare
exomes 1/1,428,916 · genomes 0/152,322 · 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
- LMF1
- Protein
- p.Pro25=
- Coding
- c.75G>C
- MANE Select
- NM_022773
- dbSNP
- rs2548412101
- Type
- single nucleotide variant
- Location
- chr16:970906 (GRCh38)
- Gene constraint
- LOEUF 1.436 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.49
- Residue 25
- the 'disordered' region
Similar variants
- LMF1 p.Arg233Ter Pathogenic/Likely pathogenic ★★ same type
- LMF1 p.Gln299Ter Pathogenic/Likely pathogenic ★★ same type
- LMF1 p.Gln422Ter Pathogenic/Likely pathogenic ★★ same type
- LMF1 p.Gly172Arg Likely pathogenic ★★ same type
- LMF1 p.Ser120Ter Pathogenic/Likely pathogenic ★★ same type
- LMF1 p.Ser137Leu Likely pathogenic ★★ same type
- LMF1 p.Trp313Ter Pathogenic/Likely pathogenic ★★ same type
- LMF1 p.Trp464Ter 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/lmf1-p-pro25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown