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): 16:83968243-84002776

Previous symbols: [ "EFCBP2" ]

Links

ENSG00000103154 ∙ NCBI:54550 ∙ OMIM:618130 ∙ HGNC:23746 ∙ Uniprot:Q7Z6G3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	2		53
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	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: gnomAD

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: 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
• 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