NECAB3
Basic information
Region (hg38): 20:33657087-33674463
Previous symbols: [ "SYTIP2", "APBA2BP" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (115 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NECAB3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031232.4. 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 | 51 | 56 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 51 | 5 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
NECAB3 | protein_coding | protein_coding | ENST00000246190 | 12 | 17377 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000275 | 0.985 | 124778 | 0 | 18 | 124796 | 0.0000721 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.964 | 179 | 219 | 0.817 | 0.0000139 | 2510 |
Missense in Polyphen | 59 | 79.019 | 0.74665 | 949 | ||
Synonymous | 0.357 | 86 | 90.3 | 0.952 | 0.00000567 | 791 |
Loss of Function | 2.18 | 11 | 22.0 | 0.500 | 0.00000103 | 257 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000228 | 0.000211 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000223 | 0.000223 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000646 | 0.0000618 |
Middle Eastern | 0.000223 | 0.000223 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibits the interaction of APBA2 with amyloid-beta precursor protein (APP), and hence allows formation of amyloid- beta. May enhance the activity of HIF1A and thus promote glycolysis under normoxic conditions; the function requires its ABM domain and may implicate the stabilization of the interaction between HIF1AN and APBA3. {ECO:0000269|PubMed:10833507, ECO:0000269|PubMed:26948053}.;
Recessive Scores
- pRec
- 0.0899
Haploinsufficiency Scores
- pHI
- 0.206
- hipred
- Y
- hipred_score
- 0.682
- ghis
- 0.411
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.503
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Necab3
- Phenotype
Gene ontology
- Biological process
- protein secretion;protein metabolic process;regulation of amyloid precursor protein biosynthetic process
- Cellular component
- Golgi cis cisterna;nucleus;cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus
- Molecular function
- calcium ion binding;protein binding