GeneBe

EMD

protein-coding

emerin, the group of LEM domain containing

Gene summary

Emerin is a serine-rich nuclear membrane protein and a member of the nuclear lamina-associated protein family. It mediates membrane anchorage to the cytoskeleton. Dreifuss-Emery muscular dystrophy is an X-linked inherited degenerative myopathy resulting from mutation in the emerin gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_000117.3

Inheritance

XL, XLR

ClinVar variants

P:108U:227B:195

Top phenotype

Emery-Dreifuss muscular dystrophy 1, X-linked

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:154,379,273-154,381,574

External References & Databases

Ensembl (ENSG00000102119)NCBI Gene (2010)OMIM (300384)HGNC:3331GenCCUniProt (P50402)AlphaFoldClinVar (EMD)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~2.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

X-linked Emery-Dreifuss muscular dystrophySTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0010680

Submitter: Labcorp Genetics (formerly Invitae)

heart conduction diseaseSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0000992

Submitter: Genomics England PanelApp

X-linked Emery-Dreifuss muscular dystrophySUPPORTIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010680

Submitter: Orphanet

X-linked Emery-Dreifuss muscular dystrophyDEFINITIVE

Inheritance Pattern: XLR

Disease ID:MONDO:0010680

Submitter: Natera

X-linked Emery-Dreifuss muscular dystrophyDEFINITIVE

Inheritance Pattern: XL

Disease ID:MONDO:0010680

Submitter: Ambry Genetics

Emery-Dreifuss muscular dystrophy 1, X-linkedSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0100531

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Emery-Dreifuss muscular dystrophy 1, X-linkedXL

Manifestation: Cardiovascular; Musculoskeletal

Intervention: Cardiovascular

Rationale: Surveillance for and treatment of cardiac disease (eg, with EKG), including pacemaker implantation, may be beneficial

Comments: Individuals, including females, can have serious cardiac conduction defects

Refs: 4567289; 3319295; 2685312; 7894480; 9195226; 10377322; 10323252; 10382910; 20301609; 21496632; 21697856Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EMD variants in ClinVar

19 Conditions Cataloged
X-linked Emery-Dreifuss muscular dystrophyTotal: 551
Cardiovascular phenotypeTotal: 150
not providedTotal: 133
not specifiedTotal: 76
Emery-Dreifuss muscular dystrophyTotal: 67
Emery-Dreifuss muscular dystrophy 1, X-linkedTotal: 50
CardiomyopathyTotal: 15
EMD-related disorderTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000117.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
8
clinvar
154
clinvar
1
clinvar
 163
missense
2
clinvar
6
clinvar
205
clinvar
38
clinvar
2
clinvar
 253
nonsense
22
clinvar
5
clinvar
1
clinvar
 28
start loss
4
clinvar
 4
frameshift
40
clinvar
12
clinvar
2
clinvar
 54
splice donor/acceptor (+/-2bp)
9
clinvar
8
clinvar
11
clinvar
 28
Total77312271923530

Highest pathogenic variant AF is 0.000008866506

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000117.3RefSeqNP_000108.16MANE Select
ENST00000369842.9EnsemblENSP00000358857.46MANE Select
ENST00000369835.3EnsemblENSP00000358850.35Standard
ENST00000369835.4EnsemblENSP00000358850.35Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Dilated cardiomyopathy (DCM) - Homo sapiens (human)
  • Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human)
  • Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human)
  • Arrhythmogenic Right Ventricular Cardiomyopathy
  • Clearance of Nuclear Envelope Membranes from Chromatin

Biological Process

  • muscle contraction
  • mitotic nuclear envelope reassembly
  • muscle organ development
  • skeletal muscle cell differentiation
  • positive regulation of protein export from nucleus

Molecular Function

  • actin binding
  • protein binding
  • cadherin binding
  • beta-tubulin binding

Cellular Component

  • nuclear envelope
  • nuclear inner membrane
  • nuclear outer membrane
  • nucleoplasm
  • cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000369842
Coding exons
6
Length
2327
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.1651151101.040.000008861642
Missense (PolyPhen)3237.2780.85842558
Synonymous-2.426443.71.470.00000335511
Loss of Function2.7108.550.005.43e-7152

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Stabilizes and promotes the formation of a nuclear actin cortical network. Stimulates actin polymerization in vitro by binding and stabilizing the pointed end of growing filaments. Inhibits beta-catenin activity by preventing its accumulation in the nucleus. Acts by influencing the nuclear accumulation of beta- catenin through a CRM1-dependent export pathway. Links centrosomes to the nuclear envelope via a microtubule association. EMD and BAF are cooperative cofactors of HIV-1 infection. Association of EMD with the viral DNA requires the presence of BAF and viral integrase. The association of viral DNA with chromatin requires the presence of BAF and EMD. Required for proper localization of non-farnesylated prelamin-A/C. {ECO:0000269|PubMed:15328537, ECO:0000269|PubMed:16680152, ECO:0000269|PubMed:16858403, ECO:0000269|PubMed:17785515, ECO:0000269|PubMed:19323649}.;
Disease
DISEASE: Emery-Dreifuss muscular dystrophy 1, X-linked (EDMD1) [MIM:310300]: A form of Emery-Dreifuss muscular dystrophy, a degenerative myopathy characterized by weakness and atrophy of muscle without involvement of the nervous system, early contractures of the elbows, Achilles tendons and spine, and cardiomyopathy associated with cardiac conduction defects. {ECO:0000269|PubMed:10323252, ECO:0000269|PubMed:11587540, ECO:0000269|PubMed:15009215, ECO:0000269|PubMed:15328537}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.537

Intolerance Scores

RVIS EVS
-0.05
RVIS percentile EVS
49.76

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.493

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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