LBR p.Pro391=
c.1173C>T · rs764872060 · VCV2985063
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, 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 -15 | GERP -5.3 |
| Overall | ||
| CADD | 0.112 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,980 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000744%
12/1,612,476 alleles · very rare
exomes 9/1,460,366 · genomes 3/152,110 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,993 |
| South Asian | 0.0022% | 45,518 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,442 |
| European (non-Finnish) | 0.000509% | 196,451 |
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
- LBR
- Protein
- p.Pro391=
- Coding
- c.1173C>T
- MANE Select
- NM_002296
- dbSNP
- rs764872060
- Type
- single nucleotide variant
- Location
- chr1:225411352 (GRCh38)
- Gene constraint
- LOEUF 0.499 · pLI 0.97 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 76.89 · 1 PDB
- Residue 391
- a UniProt-annotated variant site (in skpha)
Similar variants
- LBR c.367-2A>C Pathogenic/Likely pathogenic ★★ same type
- LBR p.Arg512Gln Pathogenic/Likely pathogenic ★★ same type
- LBR p.Arg583Gln Pathogenic ★★ same type
- LBR p.Arg586His Pathogenic/Likely pathogenic ★★ same type
- LBR p.Asn547Asp Pathogenic/Likely pathogenic ★★ same type
- LBR p.Asn547Ser Pathogenic/Likely pathogenic ★★ same type
- LBR c.*1586G>A Uncertain significance ★★ same type
- LBR p.Ala109Gly 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/lbr-p-pro391 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown