Is LMNB2 p.Asp602= (c.1806T>C) pathogenic?

LMNB2 p.Asp602= (c.1806T>C) is classified Likely benign in LMNB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-26). Very rare (popmax 0.000424%, nfe).

How common is LMNB2 p.Asp602= (c.1806T>C) in the general population?

LMNB2 p.Asp602= (c.1806T>C) is very rare (popmax 0.000424%, nfe) (gnomAD).

LMNB2 p.Asp602=

c.1806T>C · VCV4939831

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000424%, nfe)

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 -2.6
Overall
CADD	2.324	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000424% European (non-Finnish) · 5/1,179,962 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.00031% 5/1,614,048 alleles · very rare exomes 5/1,461,798 · genomes 0/152,250 · joint denominator

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.Asp602=
Coding: c.1806T>C
MANE Select: NM_032737
Type: single nucleotide variant
Location: chr19:2431563 (GRCh38)
Gene constraint: LOEUF 0.399 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 79.82 · 2 PDB
Residue 602: the 'tail' region; the 'disordered' region

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

Similar variants

LMNB2 p.Asp602Asn Uncertain significance ★ ⚠ same residue
LMNB2 p.Glu398Lys Pathogenic ★★ same type
LMNB2 c.1202+5G>A Uncertain significance ★★ same type
LMNB2 p.Ala178Thr Uncertain significance ★★ ⚠ same type
LMNB2 p.Ala299Val Uncertain significance ★★ ⚠ same type
LMNB2 p.Ala29Pro Uncertain significance ★★ ⚠ same type
LMNB2 p.Ala567Thr Uncertain significance ★★ ⚠ same type
LMNB2 p.Arg104Gly 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/lmnb2-p-asp602 (accessed [today's date]).

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