NES

nestin, the group of Intermediate filaments Type IV

Basic information

Region (hg38): 1:156668763-156677407

Links

ENSG00000132688 ∙ NCBI:10763 ∙ OMIM:600915 ∙ HGNC:7756 ∙ Uniprot:P48681 ∙ 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 NES gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NES 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				7	2	9
missense			124	17	7	148
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	124	24	9

Variants in NES

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

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

Position	Type	Phenotype	Significance	ClinVar
1-156669359-T-C		not specified	Uncertain significance (Dec 07, 2024)
1-156669408-C-A		not specified	Uncertain significance (Sep 17, 2021)
1-156669423-T-A		not specified	Uncertain significance (Jan 31, 2025)
1-156669438-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-156669466-G-A			Likely benign (Apr 09, 2018)
1-156669510-A-G		not specified	Uncertain significance (Oct 20, 2021)
1-156669579-C-T		not specified	Uncertain significance (Nov 07, 2022)
1-156669580-A-G			Likely benign (Mar 01, 2023)
1-156669606-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-156669652-T-G		not specified	Uncertain significance (Sep 01, 2021)
1-156669728-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-156669752-C-T		not specified	Likely benign (May 16, 2022)
1-156669753-C-T			Likely benign (May 21, 2018)
1-156669792-T-C			Benign (Dec 31, 2019)
1-156669825-C-G		not specified	Uncertain significance (Jan 03, 2022)
1-156669882-G-A		not specified	Uncertain significance (Nov 17, 2023)
1-156669887-G-C		not specified	Uncertain significance (Jul 30, 2024)
1-156669890-C-G		not specified	Uncertain significance (Aug 17, 2022)
1-156669926-T-C		not specified	Uncertain significance (Oct 26, 2022)
1-156669969-C-T			Benign (May 18, 2018)
1-156669971-T-C		not specified	Uncertain significance (Nov 07, 2024)
1-156669972-C-T		not specified	Uncertain significance (Dec 28, 2024)
1-156669975-G-C		not specified	Uncertain significance (Jul 14, 2021)
1-156670047-C-G		not specified	Uncertain significance (Sep 27, 2022)
1-156670081-A-C		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NES	protein_coding	protein_coding	ENST00000368223	4	8635

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000162	1.00	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.438	774	809	0.957	0.0000396	10290
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000486	0.000484
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000220	0.000217
Finnish	0.000374	0.000370
European (Non-Finnish)	0.000250	0.000246
Middle Eastern	0.000220	0.000217
South Asian	0.000534	0.000523
Other	0.000496	0.000489

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0754
• hipred: N
• hipred_score: 0.481
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.100

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nes
• Phenotype: cellular phenotype; growth/size/body region phenotype; embryo 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: nes
• Affected structure: glial cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• 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;negative regulation of protein binding;negative regulation of catalytic activity;stem cell proliferation;positive regulation of neural precursor cell proliferation
• Cellular component: cytoplasm;intermediate filament;intermediate filament cytoskeleton
• Molecular function: molecular_function;structural molecule activity;intermediate filament binding