LMNB1 p.Pro6=
c.18C>T · rs777808428 · VCV2960650
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0138%, 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 1.2 | GERP 6.9, phastCons 1 |
| Overall | ||
| CADD | 14.96 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0138%
Admixed American · 4/29,050 alleles
Filtering AF
0.0046%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00036%
5/1,388,914 alleles · ultra-rare
exomes 4/1,236,834 · genomes 1/152,080 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0138% | 7,262 |
| Remaining individualsnot grpmax-eligible | 0.0019% | 52,500 |
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
- LMNB1
- Protein
- p.Pro6=
- Coding
- c.18C>T
- MANE Select
- NM_005573
- dbSNP
- rs777808428
- Type
- single nucleotide variant
- Location
- chr5:126777526 (GRCh38)
- Gene constraint
- LOEUF 0.55 · pLI 0.87 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 82.95 · 7 PDB
- Residue 6
- the 'disordered' region; the 'head' region
Similar variants
- LMNB1 p.Pro6Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
- LMNB1 p.Arg42Trp Pathogenic/Likely pathogenic ★★ same type
- LMNB1 p.Arg90Pro Likely pathogenic ★★ same type
- LMNB1 p.Lys33Glu Pathogenic ★★ same type
- LMNB1 p.Ala15Thr Uncertain significance ★★ ⚠ same type
- LMNB1 p.Arg197His Uncertain significance ★★ ⚠ same type
- LMNB1 p.Arg208His Uncertain significance ★★ ⚠ same type
- LMNB1 p.Arg234His 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/lmnb1-p-pro6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown