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Intellectual disability

Gene: LMNA

Amber List (moderate evidence)
LMNA (lamin A/C)
EnsemblGeneIds (GRCh38): ENSG00000160789
EnsemblGeneIds (GRCh37): ENSG00000160789
OMIM: 150330, Gene2Phenotype
LMNA is in 28 panels

5 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

I don't know

Comment on publications: PMID:39767643 was identified by the Genomics England Applied Machine Learning (ML) team in a Biocuration-ML project for identifying new gene-disease associations using Natural Language Processing (NLP) and Generative AI techniques.
Created: 24 Mar 2025, 8:22 p.m. | Last Modified: 24 Mar 2025, 8:22 p.m.
Panel Version: 8.182
PMID:39767643 reported the identification of a heterozygous missense variant in LMNA gene (p. Glu443Gly) in a 16-year-old boy affected with intellectual impairment, cardiac manifestation, diabetes mellitus, a cataract in the right eye, epilepsy, and skin atrophy on his back. This family showed no positive history of neurodevelopmental disorders (NDDs) in the five previous generations, while one sibling was affected by a NDD phenotype.

There are four cases reported in the Decipher database with sequence variants in LMNA gene (https://www.deciphergenomics.org/gene/LMNA/patient-overlap/snvs) of which the patient with frameshift variant (p.Glu223AspfsTer7) was reported with a number of phenotypes including global developmental delay. This variant is annotated to be likely pathogenic and with the contribution of the variant to phenotype is uncertain.
Created: 24 Mar 2025, 8:03 p.m. | Last Modified: 24 Mar 2025, 8:08 p.m.
Panel Version: 8.180

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Publications

Created: 24 Mar 2025, 8:03 p.m.
Last Modified: 24 Mar 2025, 8:08 p.m.
Panel version: 8.178

Arina Puzriakova (Genomics England Curator)

Following discussion with the clinical team, this gene has been demoted from Amber to Red, in accordance with the external review by Zornitza Stark
Created: 17 Aug 2020, 10:09 a.m. | Last Modified: 17 Aug 2020, 10:09 a.m.
Panel Version: 3.253
Created: 17 Aug 2020, 10:09 a.m.
Last Modified: 17 Aug 2020, 10:09 a.m.
Panel version: 3.253

Zornitza Stark (Australian Genomics)

Red List (low evidence)

A number of conditions have been associated with LMNA, but intellect generally not affected.
Created: 9 Feb 2020, 7:14 a.m. | Last Modified: 9 Feb 2020, 7:14 a.m.
Panel Version: 3.0
Created: 9 Feb 2020, 7:14 a.m.
Last Modified: 9 Feb 2020, 7:14 a.m.
Panel version: 3.0

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_UKGTN_v12 . Main mutation mechanism : Loss of function; Uncertain; Activating
Created: 27 Jul 2017, 7:16 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; UKGTN_v12; neuro_20160418_strict; Loss of function; Uncertain; Activating. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 12:47 p.m.

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Publications

Created: 2 Aug 2017, 8:04 p.m.

Panel version: 1.354

Louise Daugherty (Genomics England Curator)

Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to assess inclusion and pertinence to this panel.
Created: 20 Jul 2017, 12:19 p.m.
Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to assess inclusion and pertinence to this panel.
Created: 20 Jul 2017, 12:16 p.m.
Created: 20 Jul 2017, 12:16 p.m.

Panel version: 1.207

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
Phenotypes
  • Emery-Dreifuss muscular dystrophy 2, AD, 181350
  • Cardiomyopathy, dilated, 1A, 115200
  • Lipodystrophy, familial partial, 2, 151660
  • Emery-Dreifuss muscular dystrophy 3, AR, 181350
  • Charcot-Marie-Tooth disease, type 2B1, 605588
  • Muscular dystrophy, congenital, 613205
  • Muscular dystrophy, limb-girdle, type 1B, 159001
  • Mandibuloacral dysplasia, 248370
  • Hutchinson-Gilford progeria, 176670
  • Restrictive dermopathy, lethal, 275210
  • Heart-hand syndrome, Slovenian type, 610140
  • Malouf syndrome, 212112
OMIM
150330
Clinvar variants
Variants in LMNA
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

24 Mar 2025, Gel status: 2

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: LMNA were set to 25529582; 39767643

24 Mar 2025, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: lmna has been classified as Amber List (Moderate Evidence).

24 Mar 2025, Gel status: 1

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: LMNA were set to

24 Mar 2025, Gel status: 1

Set mode of inheritance

Achchuthan Shanmugasundram (Genomics England Curator)

Mode of inheritance for gene: LMNA was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

12 Oct 2020, Gel status: 1

Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Red was added to LMNA. Rating Changed from Amber List (moderate evidence) to Red List (low evidence)

12 Mar 2018, Gel status: 2

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

20 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

20 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

19 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

LMNA was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

LMNA was created by BRIDGE