NECAB2
Basic information
Region (hg38): 16:83968244-84002776
Previous symbols: [ "EFCBP2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (110 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NECAB2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000019065.3. 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 | 0 | |||||
missense | 107 | 109 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 107 | 2 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
NECAB2 | protein_coding | protein_coding | ENST00000305202 | 13 | 34145 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.24e-13 | 0.0339 | 125695 | 0 | 53 | 125748 | 0.000211 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -4.91 | 390 | 196 | 1.99 | 0.0000121 | 2496 |
Missense in Polyphen | 167 | 91.304 | 1.8291 | 974 | ||
Synonymous | -6.92 | 160 | 80.9 | 1.98 | 0.00000522 | 752 |
Loss of Function | 0.183 | 20 | 20.9 | 0.957 | 9.77e-7 | 253 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000306 | 0.000304 |
Ashkenazi Jewish | 0.0000994 | 0.0000992 |
East Asian | 0.000272 | 0.000272 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.000247 | 0.000246 |
Middle Eastern | 0.000272 | 0.000272 |
South Asian | 0.000298 | 0.000294 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May act as a signaling scaffold protein that senses intracellular calcium. Can modulate ligand-induced internalization of ADORA2A and coupling efficiency of mGluR5/GRM5; for both receptors may regulate signaling activity such as promoting MAPK1/3 (ERK1/2) activation. {ECO:0000305|PubMed:17689978, ECO:0000305|PubMed:19694902}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.816
- rvis_EVS
- -0.13
- rvis_percentile_EVS
- 44.09
Haploinsufficiency Scores
- pHI
- 0.139
- hipred
- hipred_score
- ghis
- 0.496
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.889
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Necab2
- Phenotype
- reproductive system phenotype;
Gene ontology
- Biological process
- regulation of amyloid precursor protein biosynthetic process;positive regulation of adenosine receptor signaling pathway;positive regulation of ERK1 and ERK2 cascade;positive regulation of glutamate receptor signaling pathway;negative regulation of G protein-coupled receptor internalization;positive regulation of protein localization to membrane
- Cellular component
- cytoplasm;plasma membrane;axon;dendrite
- Molecular function
- calcium ion binding;protein binding;A2A adenosine receptor binding;type 5 metabotropic glutamate receptor binding