NEFM

neurofilament medium chain, the group of Intermediate filaments Type IV

Basic information

Region (hg38): 8:24913758-24919098

Previous symbols: [ "NEF3" ]

Links

ENSG00000104722 ∙ NCBI:4741 ∙ OMIM:162250 ∙ HGNC:7734 ∙ Uniprot:P07197 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEFM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEFM gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			60	1	1	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	1	3

Variants in NEFM

This is a list of pathogenic ClinVar variants found in the NEFM region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-24913804-C-T		not specified	Uncertain significance (Dec 11, 2024)
8-24913805-G-A			Benign (Jan 12, 2018)
8-24913824-C-G		not specified	Uncertain significance (Dec 04, 2024)
8-24913831-C-G		not specified	Uncertain significance (Mar 07, 2024)
8-24913864-T-C		not specified	Uncertain significance (Feb 12, 2024)
8-24913897-T-A			not provided (-)
8-24913917-C-G		not specified	Uncertain significance (Sep 15, 2021)
8-24913965-G-T		not specified	Uncertain significance (Jul 22, 2024)
8-24914019-G-A		not specified	Uncertain significance (Sep 13, 2023)
8-24914047-A-G		not specified	Uncertain significance (Aug 21, 2023)
8-24914154-T-C		not specified	Uncertain significance (Sep 22, 2023)
8-24914180-T-G			not provided (-)
8-24914240-G-C			not provided (-)
8-24914268-G-A		not specified	Uncertain significance (Oct 22, 2021)
8-24914296-A-G		not specified	Uncertain significance (May 30, 2024)
8-24914313-G-A		not specified	Uncertain significance (May 14, 2024)
8-24914355-C-T		not specified	Uncertain significance (Nov 12, 2024)
8-24914371-C-A		not specified	Uncertain significance (Mar 19, 2024)
8-24914403-C-G		not specified	Uncertain significance (Sep 26, 2024)
8-24914404-G-A		not specified	Uncertain significance (Feb 27, 2023)
8-24914418-G-T		not specified	Uncertain significance (Dec 11, 2024)
8-24914421-A-C		not specified	Uncertain significance (Sep 27, 2021)
8-24914454-G-A		not specified	Uncertain significance (Feb 22, 2024)
8-24914471-G-T			Benign (Dec 31, 2019)
8-24914559-G-A		not specified	Uncertain significance (Oct 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEFM	protein_coding	protein_coding	ENST00000221166	3	6083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0180	0.982	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0678	463	459	1.01	0.0000228	5962
Missense in Polyphen		63	58.208	1.0823		854
Synonymous	-0.894	209	193	1.08	0.0000105	1759
Loss of Function	3.61	9	30.5	0.295	0.00000144	456

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000637	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000559	0.0000527
Middle Eastern	0.0000637	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Neurofilaments usually contain three intermediate filament proteins: L, M, and H which are involved in the maintenance of neuronal caliber.
• Pathway: Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS);Association Between Physico-Chemical Features and Toxicity Associated Pathways (Consensus)

Recessive Scores

• pRec: 0.351

Intolerance Scores

• loftool: 0.0191
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.62

Haploinsufficiency Scores

• pHI: 0.530
• hipred: Y
• hipred_score: 0.771
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.831

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nefm
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype

Gene ontology

• Biological process: neurofilament bundle assembly;axon development
• Cellular component: neurofilament;axon;intermediate filament cytoskeleton;neurofibrillary tangle
• Molecular function: structural constituent of cytoskeleton;protein binding;microtubule binding