NECAB2

N-terminal EF-hand calcium binding protein 2, the group of N-terminal EF-hand calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 16:83968244-84002776

Previous symbols: [ "EFCBP2" ]

Links

ENSG00000103154NCBI:54550OMIM:618130HGNC:23746Uniprot:Q7Z6G3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NECAB2 gene.

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
clinvar
2
clinvar
53
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
clinvar
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)3190136
16-83968680-C-T not specified Uncertain significance (Aug 13, 2021)2351167
16-83968707-C-A not specified Uncertain significance (Aug 04, 2023)2615963
16-83968713-A-C not specified Uncertain significance (Apr 07, 2023)2534321
16-83968768-G-T not specified Uncertain significance (May 06, 2024)3299127
16-83968776-A-C not specified Uncertain significance (Apr 07, 2023)2534318
16-83968778-T-C not specified Likely benign (Apr 07, 2023)2534320
16-83968799-G-C not specified Uncertain significance (Sep 15, 2021)2249624
16-83968803-A-C not specified Uncertain significance (Aug 12, 2021)2378507
16-83968832-A-C not specified Uncertain significance (Oct 06, 2021)2229643
16-83972160-C-A not specified Uncertain significance (Jan 04, 2024)3190151
16-83972160-C-T not specified Uncertain significance (Apr 13, 2022)2236000
16-83978527-C-G not specified Uncertain significance (Oct 19, 2021)2362073
16-83978531-C-T not specified Uncertain significance (Sep 27, 2022)2398772
16-83981071-G-C not specified Uncertain significance (Aug 12, 2021)2243222
16-83981077-C-G not specified Uncertain significance (Apr 07, 2022)3190162
16-83981084-C-A not specified Uncertain significance (May 08, 2024)3299128
16-83990522-A-G not specified Uncertain significance (Sep 20, 2023)3190164
16-83990531-C-T not specified Uncertain significance (Jan 23, 2024)3190165
16-83990552-C-A not specified Uncertain significance (Jan 03, 2024)3190167
16-83990552-C-T not specified Uncertain significance (Nov 08, 2022)2402071
16-83990558-A-G not specified Uncertain significance (Feb 28, 2024)2260407
16-83990560-C-G not specified Uncertain significance (Mar 04, 2024)3190173
16-83990591-G-A not specified Uncertain significance (Sep 07, 2022)2377520
16-83990615-A-T not specified Uncertain significance (Jan 29, 2024)3190177

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NECAB2protein_codingprotein_codingENST00000305202 1334145
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.24e-130.03391256950531257480.000211
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-4.913901961.990.00001212496
Missense in Polyphen16791.3041.8291974
Synonymous-6.9216080.91.980.00000522752
Loss of Function0.1832020.90.9579.77e-7253

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003060.000304
Ashkenazi Jewish0.00009940.0000992
East Asian0.0002720.000272
Finnish0.0001390.000139
European (Non-Finnish)0.0002470.000246
Middle Eastern0.0002720.000272
South Asian0.0002980.000294
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

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