NECAB3

N-terminal EF-hand calcium binding protein 3, the group of N-terminal EF-hand calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 20:33657087-33674463

Previous symbols: [ "SYTIP2", "APBA2BP" ]

Links

ENSG00000125967NCBI:63941OMIM:612478HGNC:15851Uniprot:Q96P71AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NECAB3 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
0
missense
51
clinvar
5
clinvar
56
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 51 5 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NECAB3protein_codingprotein_codingENST00000246190 1217377
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00002750.9851247780181247960.0000721
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9641792190.8170.00001392510
Missense in Polyphen5979.0190.74665949
Synonymous0.3578690.30.9520.00000567791
Loss of Function2.181122.00.5000.00000103257

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002280.000211
Ashkenazi Jewish0.000.00
East Asian0.0002230.000223
Finnish0.000.00
European (Non-Finnish)0.00006460.0000618
Middle Eastern0.0002230.000223
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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