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
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.
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 | 51 | 53 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 2 | |||||
Total | 0 | 0 | 53 | 2 | 1 |
Variants in NECAB2
This is a list of pathogenic ClinVar variants found in the NECAB2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-83968659-G-C | not specified | Uncertain significance (Dec 17, 2023) | ||
16-83968680-C-T | not specified | Uncertain significance (Aug 13, 2021) | ||
16-83968707-C-A | not specified | Uncertain significance (Aug 04, 2023) | ||
16-83968713-A-C | not specified | Uncertain significance (Apr 07, 2023) | ||
16-83968768-G-T | not specified | Uncertain significance (May 06, 2024) | ||
16-83968776-A-C | not specified | Uncertain significance (Apr 07, 2023) | ||
16-83968778-T-C | not specified | Likely benign (Apr 07, 2023) | ||
16-83968799-G-C | not specified | Uncertain significance (Sep 15, 2021) | ||
16-83968803-A-C | not specified | Uncertain significance (Aug 12, 2021) | ||
16-83968832-A-C | not specified | Uncertain significance (Oct 06, 2021) | ||
16-83972160-C-A | not specified | Uncertain significance (Jan 04, 2024) | ||
16-83972160-C-T | not specified | Uncertain significance (Apr 13, 2022) | ||
16-83978527-C-G | not specified | Uncertain significance (Oct 19, 2021) | ||
16-83978531-C-T | not specified | Uncertain significance (Sep 27, 2022) | ||
16-83981071-G-C | not specified | Uncertain significance (Aug 12, 2021) | ||
16-83981077-C-G | not specified | Uncertain significance (Apr 07, 2022) | ||
16-83981084-C-A | not specified | Uncertain significance (May 08, 2024) | ||
16-83990522-A-G | not specified | Uncertain significance (Sep 20, 2023) | ||
16-83990531-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
16-83990552-C-A | not specified | Uncertain significance (Jan 03, 2024) | ||
16-83990552-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
16-83990558-A-G | not specified | Uncertain significance (Feb 28, 2024) | ||
16-83990560-C-G | not specified | Uncertain significance (Mar 04, 2024) | ||
16-83990591-G-A | not specified | Uncertain significance (Sep 07, 2022) | ||
16-83990615-A-T | not specified | Uncertain significance (Jan 29, 2024) |
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