NLE1

notchless homolog 1, the group of WD repeat domain containing

Basic information

Region (hg38): 17:35128730-35142304

Previous symbols: [ "NLE" ]

Links

ENSG00000073536 ∙ NCBI:54475 ∙ ∙ HGNC:19889 ∙ Uniprot:Q9NVX2 ∙ 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 NLE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NLE1 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						0
missense			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15	4	1	20
Total	0	0	50	5	1

Variants in NLE1

This is a list of pathogenic ClinVar variants found in the NLE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-35129437-G-A		not specified	Uncertain significance (Feb 27, 2025)
17-35129456-T-G		not specified	Uncertain significance (Apr 10, 2023)
17-35129470-C-T		not specified	Uncertain significance (May 16, 2024)
17-35129515-G-A		not specified	Likely benign (Dec 06, 2021)
17-35129518-G-A		not specified	Uncertain significance (Mar 04, 2025)
17-35129621-A-G		not specified	Uncertain significance (Nov 17, 2023)
17-35129632-G-A		not specified	Uncertain significance (Jan 02, 2024)
17-35129645-G-A		not specified	Uncertain significance (Jul 02, 2024)
17-35130298-C-T		not specified	Uncertain significance (Jun 18, 2021)
17-35130348-C-G		not specified	Uncertain significance (Dec 27, 2023)
17-35130349-G-A		not specified	Uncertain significance (Dec 09, 2024)
17-35130361-G-A		not specified	Likely benign (Dec 15, 2022)
17-35130372-G-A		not specified	Uncertain significance (Jul 31, 2024)
17-35130375-T-C		not specified	Uncertain significance (Oct 01, 2024)
17-35130378-A-G		not specified	Uncertain significance (Jul 14, 2024)
17-35130381-G-A		not specified	Likely benign (Jan 23, 2023)
17-35130397-G-A		not specified	Uncertain significance (Feb 28, 2025)
17-35130414-G-A		not specified	Uncertain significance (Dec 28, 2023)
17-35132441-C-T		not specified	Uncertain significance (Jul 09, 2021)
17-35133222-C-G		not specified	Uncertain significance (Jun 28, 2024)
17-35133363-C-T		not specified	Uncertain significance (Nov 09, 2023)
17-35133364-A-G		not specified	Likely benign (Nov 09, 2021)
17-35133386-C-T		not specified	Uncertain significance (May 30, 2022)
17-35133436-C-T		not specified	Uncertain significance (Jan 22, 2024)
17-35135255-G-A		not specified	Uncertain significance (May 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NLE1	protein_coding	protein_coding	ENST00000442241	13	13563

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000296	0.999	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.563	271	298	0.908	0.0000178	3121
Missense in Polyphen		92	115.61	0.79576		1197
Synonymous	0.740	112	122	0.915	0.00000727	991
Loss of Function	3.02	11	28.3	0.388	0.00000149	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000528	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in regulating Notch activity. Plays a role in regulating the expression of CDKN1A and several members of the Wnt pathway, probably via its effects on Notch activity. Required during embryogenesis for inner mass cell survival (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.723
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.66

Haploinsufficiency Scores

• pHI: 0.269
• hipred: Y
• hipred_score: 0.704
• ghis: 0.408

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nle1
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; embryo phenotype; immune system phenotype; digestive/alimentary phenotype; 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); hematopoietic system phenotype

Gene ontology

• Biological process: ribosomal large subunit assembly;somitogenesis;kidney development;inner cell mass cell differentiation;Notch signaling pathway;negative regulation of mitotic cell cycle;skeletal system morphogenesis;hematopoietic stem cell homeostasis;positive regulation of canonical Wnt signaling pathway;negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway
• Cellular component: nucleus;nucleolus