Is LMNA p.Ser71= (c.213C>T) pathogenic?

LMNA p.Ser71= (c.213C>T) is classified Likely benign in LMNA (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-22). Absent from gnomAD v4.1; Associated with cardiomyopathy.

What condition is associated with LMNA p.Ser71= (c.213C>T)?

LMNA p.Ser71= (c.213C>T) is associated with cardiomyopathy (ClinVar).

How common is LMNA p.Ser71= (c.213C>T) in the general population?

LMNA p.Ser71= (c.213C>T) is absent from gnomAD v4.1 (gnomAD).

LMNA p.Ser71=

c.213C>T · VCV3894340

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

cardiomyopathy

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 0.79	GERP -0.9, phastCons 1
Overall
CADD	13.64	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: LMNA
Protein: p.Ser71=
Coding: c.213C>T
MANE Select: NM_170707
Type: single nucleotide variant
Location: chr1:156115131 (GRCh38)
Gene constraint: LOEUF 0.412 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.55 · 28 PDB
Residue 71: the 'linker 1' region; an α-helix; a modified residue (phosphoserine); the if rod domain; the 'interaction with mlip' region

Full LMNA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cardiomyopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LMNA p.Ser71Ile Uncertain significance ★★ ⚠ same residue
LMNA p.Ser71Arg Uncertain significance ★ ⚠ same residue
LMNA p.Ser71Cys Uncertain significance ★ ⚠ same residue
LMNA p.Ser71Thr Uncertain significance ★ ⚠ same residue
LMNA c.639+1G>A Likely pathogenic ★★ same condition
LMNA p.Arg190Gln Pathogenic/Likely pathogenic ★★ same condition
LMNA p.Arg225Ter Pathogenic/Likely pathogenic ★★ same condition
LMNA p.Arg249Gln 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-ser71 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown