NID1
Basic information
Region (hg38): 1:235975830-236065109
Previous symbols: [ "NID" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (182 variants)
- not_provided (41 variants)
- Cerebellar_dysfunction_with_variable_cognitive_and_behavioral_abnormalities (2 variants)
- Hemiparesis (1 variants)
- Hydrocephalus (1 variants)
- Focal_epilepsy (1 variants)
- Variant_of_unknown_significance (1 variants)
- Inborn_genetic_diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NID1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002508.3. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 17 | |||||
missense | 176 | 11 | 196 | |||
nonsense | 2 | |||||
start loss | 1 | 1 | ||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 2 | 179 | 20 | 17 |
Highest pathogenic variant AF is 0.0000131456
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
NID1 | protein_coding | protein_coding | ENST00000264187 | 20 | 89333 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
7.22e-12 | 1.00 | 125685 | 1 | 62 | 125748 | 0.000251 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.482 | 743 | 781 | 0.951 | 0.0000489 | 8076 |
Missense in Polyphen | 194 | 244.97 | 0.79193 | 2536 | ||
Synonymous | -0.204 | 347 | 342 | 1.01 | 0.0000244 | 2540 |
Loss of Function | 3.78 | 29 | 60.8 | 0.477 | 0.00000342 | 627 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000815 | 0.000814 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000436 | 0.000435 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000205 | 0.000202 |
Middle Eastern | 0.000436 | 0.000435 |
South Asian | 0.000490 | 0.000457 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Sulfated glycoprotein widely distributed in basement membranes and tightly associated with laminin. Also binds to collagen IV and perlecan. It probably has a role in cell- extracellular matrix interactions.;
- Pathway
- Laminin interactions;Extracellular matrix organization;Degradation of the extracellular matrix;Beta1 integrin cell surface interactions
(Consensus)
Recessive Scores
- pRec
- 0.351
Intolerance Scores
- loftool
- 0.0768
- rvis_EVS
- 0.45
- rvis_percentile_EVS
- 77.93
Haploinsufficiency Scores
- pHI
- 0.785
- hipred
- Y
- hipred_score
- 0.602
- ghis
- 0.604
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.862
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | Medium | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Nid1
- Phenotype
- cellular phenotype; muscle phenotype; vision/eye 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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
- cell-matrix adhesion;positive regulation of cell-substrate adhesion;extracellular matrix organization;glomerular basement membrane development;basement membrane organization
- Cellular component
- extracellular region;basement membrane;collagen-containing extracellular matrix;extracellular exosome;cell periphery
- Molecular function
- extracellular matrix structural constituent;calcium ion binding;collagen binding;laminin binding;laminin-1 binding;proteoglycan binding