NELL1

neural EGFL like 1

Basic information

Region (hg38): 11:20669550-21575686

Links

ENSG00000165973 ∙ NCBI:4745 ∙ OMIM:602319 ∙ HGNC:7750 ∙ Uniprot:Q92832 ∙ 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 NELL1 gene.

• Inborn genetic diseases (32 variants)
• not provided (16 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NELL1 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				3	2	5
missense			33	1	8	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	33	4	10

Variants in NELL1

This is a list of pathogenic ClinVar variants found in the NELL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-20677949-G-A		not specified	Uncertain significance (Jun 29, 2022)
11-20678000-A-G		not specified	Uncertain significance (Dec 21, 2022)
11-20678030-C-T		not specified	Uncertain significance (Nov 03, 2022)
11-20678032-C-G		not specified	Uncertain significance (Sep 20, 2023)
11-20678049-T-G		not specified	Uncertain significance (Jan 02, 2024)
11-20783706-C-T		not specified	Uncertain significance (Jan 23, 2024)
11-20783739-C-T		not specified	Uncertain significance (Aug 19, 2021)
11-20783744-C-G		not specified	Uncertain significance (Jan 22, 2024)
11-20847584-T-C		not specified	Uncertain significance (Oct 27, 2023)
11-20847623-C-T		not specified	Uncertain significance (Nov 08, 2022)
11-20847624-G-A		not specified	Uncertain significance (May 18, 2023)
11-20847704-G-A			Benign (Dec 31, 2019)
11-20885476-C-T		not specified	Uncertain significance (Nov 19, 2021)
11-20885481-C-T		not specified	Uncertain significance (Feb 26, 2024)
11-20885514-C-T			Benign (Jul 06, 2018)
11-20885519-C-G		not specified	Uncertain significance (Feb 23, 2023)
11-20885535-T-C		not specified	Uncertain significance (Sep 26, 2022)
11-20918209-T-G			Benign (Dec 31, 2019)
11-20918231-C-A		not specified	Uncertain significance (Nov 21, 2023)
11-20918242-A-G		not specified	Uncertain significance (Apr 08, 2022)
11-20919245-T-C		not specified	Likely benign (Jan 02, 2020)
11-20919308-G-A		not specified	Uncertain significance (Feb 27, 2023)
11-20919317-G-T		not specified	Uncertain significance (Feb 23, 2023)
11-20919326-A-G		not specified	Uncertain significance (Feb 10, 2023)
11-20919331-A-T			Benign (Feb 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NELL1	protein_coding	protein_coding	ENST00000357134	20	906111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.67e-12	0.999	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00549	454	454	1.00	0.0000236	5356
Missense in Polyphen		121	158.61	0.76288		1923
Synonymous	-0.765	172	160	1.08	0.00000852	1449
Loss of Function	2.95	26	48.1	0.541	0.00000260	575

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000451	0.000450
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000382	0.000381
South Asian	0.000363	0.000359
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the control of cell growth and differentiation. Promotes osteoblast cell differentiation and terminal mineralization. {ECO:0000269|PubMed:21723284}.

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.295
• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.52

Haploinsufficiency Scores

• pHI: 0.163
• hipred: Y
• hipred_score: 0.604
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.448

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nell1
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; skeleton phenotype; craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: nervous system development;regulation of gene expression;cell differentiation;positive regulation of bone mineralization;negative regulation of osteoblast proliferation;positive regulation of osteoblast differentiation;negative regulation of cellular protein catabolic process
• Cellular component: extracellular region;nuclear envelope;cytoplasm;perinuclear region of cytoplasm
• Molecular function: calcium ion binding;protein binding