NELL1
Basic information
Region (hg38): 11:20669551-21575686
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 6 | |||||
missense | 55 | 64 | ||||
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 | 55 | 5 | 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) | ||
11-20677955-G-C | not specified | Uncertain significance (Aug 27, 2024) | ||
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) | ||
11-20783683-T-A | not specified | Uncertain significance (Apr 23, 2024) | ||
11-20783683-T-C | not specified | Likely benign (May 14, 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) | ||
11-20783776-A-G | not specified | Uncertain significance (Sep 08, 2024) | ||
11-20847584-T-C | not specified | Uncertain significance (Oct 27, 2023) | ||
11-20847623-C-T | not specified | Uncertain significance (Nov 26, 2024) | ||
11-20847624-G-A | not specified | Uncertain significance (May 18, 2023) | ||
11-20847704-G-A | Benign (Dec 31, 2019) | |||
11-20847705-C-T | not specified | Uncertain significance (May 26, 2024) | ||
11-20885465-C-A | not specified | Uncertain significance (Nov 26, 2024) | ||
11-20885476-C-T | not specified | Uncertain significance (Nov 11, 2024) | ||
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 (Dec 02, 2024) | ||
11-20918209-T-G | Benign (Dec 31, 2019) | |||
11-20918216-C-T | not specified | Uncertain significance (Oct 25, 2024) |
GnomAD
Source:
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:
- 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