NEURL2

neuralized E3 ubiquitin protein ligase 2

Basic information

Region (hg38): 20:45888624-45891208

Previous symbols: [ "C20orf163" ]

Links

ENSG00000124257 ∙ NCBI:140825 ∙ OMIM:608597 ∙ HGNC:16156 ∙ Uniprot:Q9BR09 ∙ 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 NEURL2 gene.

• Combined deficiency of sialidase AND beta galactosidase (8 variants)
• Inborn genetic diseases (8 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEURL2 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			8			8
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	2	1	8
Total	0	0	13	3	1

Variants in NEURL2

This is a list of pathogenic ClinVar variants found in the NEURL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45888789-T-G		not specified	Uncertain significance (Aug 02, 2022)
20-45888820-G-A		not specified	Uncertain significance (Feb 27, 2023)
20-45888864-A-C		not specified	Uncertain significance (Feb 28, 2023)
20-45888870-G-A		not specified	Uncertain significance (Jul 26, 2023)
20-45890493-G-A		not specified	Uncertain significance (Dec 20, 2023)
20-45890495-C-T		not specified	Uncertain significance (May 08, 2023)
20-45890516-A-G		not specified	Uncertain significance (Aug 15, 2023)
20-45890562-C-T		not specified	Uncertain significance (Oct 30, 2023)
20-45890565-C-T		not specified	Uncertain significance (Mar 14, 2023)
20-45890574-T-C		not specified	Likely benign (Sep 23, 2023)
20-45890585-C-CT			Likely benign (Oct 01, 2023)
20-45890622-G-A		not specified	Uncertain significance (Mar 21, 2023)
20-45890658-C-G		not specified	Uncertain significance (Sep 17, 2021)
20-45890723-G-A		not specified	Uncertain significance (Apr 25, 2022)
20-45890843-G-A		not specified	Uncertain significance (Dec 15, 2023)
20-45891004-G-A		Combined deficiency of sialidase AND beta galactosidase	Benign (Jun 28, 2018)
20-45891034-T-C		Combined deficiency of sialidase AND beta galactosidase	Uncertain significance (Jun 14, 2016)
20-45891055-G-A		Combined deficiency of sialidase AND beta galactosidase	Uncertain significance (Jun 14, 2016)
20-45891082-TC-T		Combined deficiency of sialidase AND beta galactosidase	Uncertain significance (Jun 14, 2016)
20-45891088-CT-C		Combined deficiency of sialidase AND beta galactosidase	Uncertain significance (Jun 14, 2016)
20-45891092-C-G		Combined deficiency of sialidase AND beta galactosidase	Uncertain significance (Jun 14, 2016)
20-45891103-G-A		Combined deficiency of sialidase AND beta galactosidase	Likely benign (Jun 19, 2018)
20-45891154-A-C		Combined deficiency of sialidase AND beta galactosidase	Likely benign (Jun 14, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEURL2	protein_coding	protein_coding	ENST00000372518	2	2663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000134	0.421	124681	5	1041	125727	0.00417

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.306	158	169	0.934	0.00000803	1794
Missense in Polyphen		51	55.076	0.92599		583
Synonymous	-0.690	82	74.4	1.10	0.00000343	643
Loss of Function	0.173	6	6.48	0.926	2.82e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00200	0.00191
Ashkenazi Jewish	0.00762	0.00747
East Asian	0.0000544	0.0000544
Finnish	0.00239	0.00236
European (Non-Finnish)	0.00732	0.00705
Middle Eastern	0.0000544	0.0000544
South Asian	0.00144	0.00137
Other	0.00488	0.00473

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in the process of myofiber differentiation and maturation. Probable substrate-recognition component of a SCF-like ECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin-protein ligase complex, which mediates the ubiquitination of proteins. Probably contributes to catalysis through recognition and positioning of the substrate and the ubiquitin-conjugating enzyme. During myogenesis, controls the ubiquitination and degradation of the specific pool of CTNNB1/beta-catenin located at the sarcolemma (By similarity). {ECO:0000250}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.602
• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.189
• hipred: N
• hipred_score: 0.480
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.872

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Neurl2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: protein ubiquitination;intracellular signal transduction;post-translational protein modification
• Cellular component: cytosol
• Molecular function: ubiquitin protein ligase activity