NEFH

protein-coding

neurofilament heavy chain, the group of Intermediate filaments Type IV

Gene summary

Neurofilaments are type IV intermediate filament heteropolymers composed of light, medium, and heavy chains. Neurofilaments comprise the axoskeleton and functionally maintain neuronal caliber. They may also play a role in intracellular transport to axons and dendrites. This gene encodes the heavy neurofilament protein. This protein is commonly used as a biomarker of neuronal damage and susceptibility to amyotrophic lateral sclerosis (ALS) has been associated with mutations in this gene. [provided by RefSeq, Oct 2008]

MANE transcript

NM_021076.4

Inheritance

AD

ClinVar variants

P:12U:633B:378

Top phenotype

Charcot-Marie-Tooth disease, axonal, type 2CC

gnomAD constraint

pLI —, LoF o/e 0.75

Max pathogenic AF

—

Genomic locus

chr22:29,480,218-29,491,390

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~11.2 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Charcot-Marie-Tooth disease axonal type 2CCSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014836

Submitter: PanelApp Australia

Charcot-Marie-Tooth disease axonal type 2CCSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014836

Submitter: Labcorp Genetics (formerly Invitae)

amyotrophic lateral sclerosisLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0004976

Submitter: ClinGen

*NEFH* was first reported in relation to autosomal dominant amyotrophic lateral sclerosis in 1994 (Figlewicz et al., PMID: 7849698). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found differences in molecular mechanism, inheritance pattern, and phenotypic variability (PMIDs: 27040688, 34518334, 7849698). Therefore, the following disease entities have been split into multiple disease entities, Charcot-Marie-Tooth disease, axonal, type 2CC (OMIM: 616924) and susceptibility to amyotrophic lateral sclerosis (OMIM: 105400). The split curation for autosomal dominant Charcot-Marie-Tooth disease, axonal, type 2CC has been curated separately. 20 variants (missense and large deletions) that have been reported in 20 probands in 13 publications (PMIDs: 29650794, 7849698, 9931323, 34511133, 8871580, 9875737, 21220648, 25299611, 28160950, 29411640, 31788332, 31475037, 32166880) are included in this curation. Additional variants in *NEFH* have been reported but were not scored in this curation due to high minor allele frequencies in population databases. Coding repeats in the KSP repeat region of *NEFH* affect phosphorylation and axonal integrity as the cross-bridge interaction with microtubules and other neurofilaments is destroyed, leading to cytoplasmic inclusions containing intermediate filament proteins. Missense variants residing mainly in the KSP repeat region have more recently been associated with ALS. Multiple screening and targeted sequencing panel studies have found that missense variants may modify risk for ALS. This gene-disease relationship is also supported by experimental evidence (an expression study). RT-PCR and western blot analysis showed an increase in transcript and protein levels of *NEFH* in sALS spinal cord (PMID:30029677). In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen ALS GCEP on the meeting date March 23, 2023 (SOP Version 9).

Charcot-Marie-Tooth disease axonal type 2CCDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014836

Submitter: ClinGen

NEFH was first reported to be associated with autosomal dominant Charcot-Marie-Tooth disease type 2 in 2016 (Rebelo et al., PMID:27040688). This gene has also been implicated as a risk factor in ALS. NEFH encodes for the neurofilament heavy chain, a key component of neurofilaments, essential for the formation of cytoskeleton in neurons. Clinical features of patients with NEFH mutations include sensorimotor axonal neuropathy mainly characterized by distal lower limbs motor deficit with early and prominent involvement of proximal hip muscles. Additional common features include muscle cramps and increased creatine kinase level. All reported cases have frameshift mutations that cluster at the c-terminus end of the protein. Mutations result in loss of the stop codon and translation of the 3’-UTR. NEFH mutants carry a sequence extension of 45 extra amino acids, containing an amyloidogenic motif referred as cryptic amyloidogenic element of the 3’-UTR (CAE). This type of variant has been reported in 4 additional publications (PMIDs: 28709447, 28544463, 29587262, 30992180). NEFH physically interacts with NEFL, also a known CMT gene, forming neurofilament structures. The NEFH knockout mouse model showed diminished calibers of large myelinated axons in both central and peripheral nervous systems (Eder et at, PMID: 976343). Expression of frameshift mutants in cultured cells resulted in accumulation of prominent perinuclear aggregates, disrupted neurofilaments structures and cell toxicity (PMID:27040688). Expression of NEFH mutants in zebrafish resulted in abnormal motor neurons with truncated axons. A zebrafish rescue experiment showed that the WT human NEFH mRNA can rescue the morpholino injected fish, however, NEFH frameshift mutants were not able to rescue the phenotype (PMID:28544463). Expression of CMT-NEFH mutations in chick embryos resulted in neurofilament aggregates in the soma of neurons leading to neuronal cell death. Aggregates stain positive for activated caspase 3 and the autophagy marker p62 (Jacquier et al., PMID: 28709447). In summary, NEFH genetic and functional evidence was classified as DEFINITIVE.

Clinical Genomic Database (CGD)

Charcot-Marie-Tooth disease, axonal, type 2CCAD

Manifestation: Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 27040688Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NEFH variants in ClinVar

11 Conditions Cataloged
not providedTotal: 979
Inborn genetic diseasesTotal: 245
NEFH-related disorderTotal: 170
not specifiedTotal: 76
Charcot-Marie-Tooth disease axonal type 2CCTotal: 36
Amyotrophic lateral sclerosis type 1Total: 14
Hereditary neuropathy or pain disorderTotal: 3
Peripheral neuropathyTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021076.4. 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
1
clinvar
284
clinvar
11
clinvar
296
missense
574
clinvar
72
clinvar
3
clinvar
649
nonsense
2
clinvar
18
clinvar
3
clinvar
1
clinvar
24
start loss
2
clinvar
2
frameshift
2
clinvar
6
clinvar
36
clinvar
3
clinvar
1
clinvar
48
splice donor/acceptor (+/-2bp)
2
clinvar
2
clinvar
4
Total210633362161023

Highest pathogenic variant AF is 0.0000050170506

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_021076.4RefSeqNP_066554.24MANE Select
ENST00000310624.7EnsemblENSP00000311997.64MANE Select
ENST00001132514.1EnsemblENSP00000806239.14Standard
XM_011530200.3RefSeqXP_011528502.15Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human)
  • Amyotrophic lateral sclerosis (ALS)
  • Association Between Physico-Chemical Features and Toxicity Associated Pathways

Biological Process

  • microtubule cytoskeleton organization
  • axonogenesis
  • cell projection assembly
  • neurofilament bundle assembly
  • peripheral nervous system neuron axonogenesis

Molecular Function

  • structural molecule activity
  • structural constituent of cytoskeleton
  • microtubule binding
  • kinesin binding
  • protein kinase binding

Cellular Component

  • cytoplasm
  • cytoskeleton
  • neurofilament
  • postsynaptic density
  • axon

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000310624
Coding exons
4
Length
11161
Individuals with no LoFs
125695
Homozygous LoFs
0
Heterozygous LoFs
53
Defined
125748
p
0.000211
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.5234705030.9340.00002636534
Missense (PolyPhen)3225.7771.2414350
Synonymous-0.5202232131.050.00001202008
Loss of Function1.282229.50.7450.00000145469

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000490.00049rare
Latino/Admixed American0.000260.00023rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000330.00033rare
Finnish0.000280.00028rare
European (Non-Finnish)0.000170.00017rare
South Asian0.000130.00013rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Neurofilaments usually contain three intermediate filament proteins: L, M, and H which are involved in the maintenance of neuronal caliber. NF-H has an important function in mature axons that is not subserved by the two smaller NF proteins.;
Disease
DISEASE: Amyotrophic lateral sclerosis (ALS) [MIM:105400]: A neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5- 10% of the cases. {ECO:0000269|PubMed:7849698}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Charcot-Marie-Tooth disease 2CC (CMT2CC) [MIM:616924]: An axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. {ECO:0000269|PubMed:27040688}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.212

Intolerance Scores

LoFtool
0.0978
RVIS EVS
0.25
RVIS percentile EVS
69.57

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.611

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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