NES

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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				8 clinvar	2 clinvar	10
missense			218 clinvar	23 clinvar	6 clinvar	247
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	218	31	8	257

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006617.2	RefSeq	NP_006608.1	4	MANE Select
ENST00000368223.4	Ensembl	ENSP00000357206.3	4	MANE Select
ENST00000867897.1	Ensembl	ENSP00000537956.1	4	Standard
ENST00000867897.2	Ensembl	ENSP00000537956.1	4	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
nes	Danio rerio	Structure: glial cell Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

nes

Danio rerio

Structure: glial cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

G2/M transition of mitotic cell cycle
central nervous system development
brain development
positive regulation of intermediate filament depolymerization
embryonic camera-type eye development

Molecular Function

molecular_function
structural molecule activity
intermediate filament binding

Cellular Component

cytoplasm
intermediate filament
intermediate filament cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368223
Coding exons: 4
Length: 8635
Individuals with no LoFs: 125677
Homozygous LoFs: 0
Heterozygous LoFs: 71
Defined: 125748
p: 0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.438	774	809	0.957	0.0000396	10290
Missense (PolyPhen)		146	187.79	0.77747		2494
Synonymous	0.607	330	344	0.958	0.0000173	3396
Loss of Function	4.30	20	54.1	0.370	0.00000256	672

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.00025	0.00025	rare
South Asian	0.00053	0.00052	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for brain and eye development. Promotes the disassembly of phosphorylated vimentin intermediate filaments (IF) during mitosis and may play a role in the trafficking and distribution of IF proteins and other cellular factors to daughter cells during progenitor cell division. Required for survival, renewal and mitogen-stimulated proliferation of neural progenitor cells (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.651

Intolerance Scores

LoFtool: 0.0569
RVIS EVS: 0.97
RVIS percentile EVS: 90.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.100

Gene Damage Prediction

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