NELL2

neural EGFL like 2

Basic information

Region (hg38): 12:44508275-44921848

Links

ENSG00000184613 ∙ NCBI:4753 ∙ OMIM:602320 ∙ HGNC:7751 ∙ Uniprot:Q99435 ∙ 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 NELL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NELL2 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			47			47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	48	0	0

Variants in NELL2

This is a list of pathogenic ClinVar variants found in the NELL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-44520015-C-T		not specified	Uncertain significance (Apr 08, 2022)
12-44520075-A-G		not specified	Uncertain significance (Jan 06, 2023)
12-44520079-C-T		not specified	Uncertain significance (Feb 06, 2024)
12-44520094-T-C		not specified	Uncertain significance (Aug 14, 2023)
12-44520109-G-A		not specified	Uncertain significance (Dec 08, 2023)
12-44520147-G-A		not specified	Uncertain significance (Jan 16, 2024)
12-44522007-C-T		not specified	Uncertain significance (Jun 24, 2022)
12-44522016-T-A		not specified	Uncertain significance (Feb 03, 2022)
12-44522120-A-T		not specified	Uncertain significance (Jun 11, 2021)
12-44522143-C-T		not specified	Uncertain significance (May 31, 2023)
12-44522154-C-T		not specified	Uncertain significance (Jan 26, 2022)
12-44523298-G-A		not specified	Uncertain significance (Oct 27, 2022)
12-44523393-A-C		not specified	Uncertain significance (Oct 25, 2022)
12-44523403-C-T		not specified	Uncertain significance (Dec 17, 2021)
12-44532589-G-A		not specified	Uncertain significance (Jan 09, 2024)
12-44532602-G-A		not specified	Uncertain significance (Nov 08, 2022)
12-44532631-T-A		not specified	Uncertain significance (Jan 03, 2024)
12-44532679-C-T		not specified	Uncertain significance (Feb 21, 2024)
12-44607213-A-G		not specified	Uncertain significance (Nov 30, 2021)
12-44607231-G-A		not specified	Uncertain significance (Mar 24, 2023)
12-44610946-T-C		not specified	Uncertain significance (Feb 15, 2023)
12-44665516-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-44665585-C-T		not specified	Uncertain significance (Oct 22, 2021)
12-44665604-C-A		not specified	Uncertain significance (Nov 07, 2022)
12-44665604-C-T		not specified	Uncertain significance (Mar 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NELL2	protein_coding	protein_coding	ENST00000437801	21	413574

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000479	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.730	435	480	0.906	0.0000245	5744
Missense in Polyphen		141	189.61	0.74364		2288
Synonymous	0.00238	170	170	1.00	0.00000880	1549
Loss of Function	5.84	7	52.9	0.132	0.00000285	611

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for neuron survival through the modulation of MAPK pathways (By similarity). Involved in the regulation of hypothalamic GNRH secretion and the control of puberty (By similarity). {ECO:0000250|UniProtKB:Q62918}.
• Pathway: Developmental Biology;Regulation of commissural axon pathfinding by SLIT and ROBO;Signaling by ROBO receptors;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.0196
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.47

Haploinsufficiency Scores

• pHI: 0.358
• hipred: Y
• hipred_score: 0.687
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.582

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nell2
• 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)

Gene ontology

• Biological process: neuron cellular homeostasis
• Cellular component: extracellular region;cell
• Molecular function: calcium ion binding;protein binding