LMF1 p.Pro27=
c.81T>C · rs371796784 · VCV1201288
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.455%, afr)
Conditions
1
Cardiovascular phenotype
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 -6.2 | GERP -1.8 |
| Overall | ||
| CADD | 1.211 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.455%
African / African-American · 330/72,500 alleles
Filtering AF
0.415%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.399%
Overall
0.0238%
376/1,580,082 alleles · rare
exomes 171/1,427,904 · genomes 205/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.455% | 220 |
| Remaining individualsnot grpmax-eligible | 0.0475% | 2,107 |
| Admixed American | 0.0281% | 3,564 |
| South Asian | 0.00116% | 86,074 |
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.Pro27=
- Coding
- c.81T>C
- MANE Select
- NM_022773
- dbSNP
- rs371796784
- Type
- single nucleotide variant
- Location
- chr16:970900 (GRCh38)
- Gene constraint
- LOEUF 1.436 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.49
- Residue 27
- the 'disordered' region
Similar variants
- LMF1 p.Pro27His Uncertain significance ★ ⚠ same residue
- LMF1 p.Arg233Ter Pathogenic/Likely pathogenic ★★ same condition
- LMF1 p.Gln299Ter Pathogenic/Likely pathogenic ★★ same condition
- LMF1 p.Ala252Val Uncertain significance ★★ same condition
- LMF1 p.Ala429Val Uncertain significance ★★ ⚠ same condition
- LMF1 p.Ala469Val Uncertain significance ★★ ⚠ same condition
- LMF1 p.Ala494Gly Uncertain significance ★★ ⚠ same condition
- LMF1 p.Ala499Val Uncertain significance ★★ ⚠ same condition
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-pro27 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown