Is LMNB2 p.Ser37= (c.111G>A) pathogenic?

LMNB2 p.Ser37= (c.111G>A) is classified Likely benign in LMNB2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-02-24). Rare (popmax 0.153%, mid); Associated with lipodystrophy, partial, acquired, susceptibility to.

What condition is associated with LMNB2 p.Ser37= (c.111G>A)?

LMNB2 p.Ser37= (c.111G>A) is associated with lipodystrophy, partial, acquired, susceptibility to, progressive myoclonic epilepsy type 9 (ClinVar).

How common is LMNB2 p.Ser37= (c.111G>A) in the general population?

LMNB2 p.Ser37= (c.111G>A) is rare (popmax 0.153%, mid) (gnomAD).

LMNB2 p.Ser37=

c.111G>A · rs770940136 · VCV1137984

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.153%, mid)

Conditions

lipodystrophy, partial, acquired, susceptibility to

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 -0.041	GERP -1.8, phastCons 0.8
Overall
CADD	12.98	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.153% Middle Eastern · 6/3,930 alleles

Filtering AF 0.0665% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0454%

Overall 0.00133% 19/1,429,678 alleles · rare exomes 17/1,279,544 · genomes 2/150,134 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.153%	655
Admixed American	0.00231%	43,212
Remaining individualsnot grpmax-eligible	0.00191%	52,402
African / African-American	0.00148%	67,410
European (non-Finnish)	0.000925%	108,077

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: LMNB2
Protein: p.Ser37=
Coding: c.111G>A
MANE Select: NM_032737
dbSNP: rs770940136
Type: single nucleotide variant
Location: chr19:2456823 (GRCh38)
Gene constraint: LOEUF 0.399 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 79.82 · 2 PDB
Residue 37: a modified residue (phosphoserine); the 'head' region; the 'disordered' region

Full LMNB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

lipodystrophy, partial, acquired, susceptibility to — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: progressive myoclonic epilepsy type 9

Similar variants

LMNB2 c.1202+5G>A Uncertain significance ★★ same condition
LMNB2 p.Ala178Thr Uncertain significance ★★ ⚠ same condition
LMNB2 p.Ala299Val Uncertain significance ★★ ⚠ same condition
LMNB2 p.Ala29Pro Uncertain significance ★★ ⚠ same condition
LMNB2 p.Ala567Thr Uncertain significance ★★ ⚠ same condition
LMNB2 p.Arg104Gly Uncertain significance ★★ ⚠ same condition
LMNB2 p.Arg114His Uncertain significance ★★ ⚠ same condition
LMNB2 p.Arg148Cys 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/lmnb2-p-ser37 (accessed [today's date]).

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