LMNA p.Pro658=
c.1974C>T · VCV3538718
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.84e-05%)
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 2.6 | GERP 0.89, phastCons 1 |
| Overall | ||
| CADD | 10.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.84e-05%
Overall
6.84e-05%
1/1,461,828 alleles · very rare
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
- LMNA
- Protein
- p.Pro658=
- Coding
- c.1974C>T
- MANE Select
- NM_170707
- Type
- single nucleotide variant
- Location
- chr1:156139085 (GRCh38)
- Gene constraint
- LOEUF 0.412 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.55 · 28 PDB
- Residue 658
- the 'tail' region
Similar variants
- LMNA p.Pro658Leu Uncertain significance ★ ⚠ same residue
- LMNA c.1157+1G>A Pathogenic/Likely pathogenic ★★ same condition
- LMNA c.1380+1G>A Pathogenic ★★ same condition
- LMNA c.1608+2T>C Likely pathogenic ★★ same condition
- LMNA c.1608+2T>G Pathogenic/Likely pathogenic ★★ same condition
- LMNA c.639+1G>T Likely pathogenic ★★ same condition
- LMNA c.640-10A>G Pathogenic/Likely pathogenic ★★ same condition
- LMNA c.811-1G>A Pathogenic/Likely pathogenic ★★ 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/lmna-p-pro658 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown