NUCB2

nucleobindin 2, the group of EF-hand domain containing

Basic information

Region (hg38): 11:17208153-17349980

Links

ENSG00000070081 ∙ NCBI:4925 ∙ OMIM:608020 ∙ HGNC:8044 ∙ Uniprot:P80303 ∙ 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 NUCB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUCB2 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in NUCB2

This is a list of pathogenic ClinVar variants found in the NUCB2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-17276557-A-C			not provided (-)
11-17276578-C-G		not specified	Conflicting classifications of pathogenicity (Oct 28, 2020)
11-17276676-G-A			not provided (-)
11-17276730-A-G			not provided (-)
11-17276818-G-C			not provided (-)
11-17295372-T-C		not specified	Uncertain significance (Oct 20, 2023)
11-17295385-C-T		not specified	Uncertain significance (Nov 09, 2021)
11-17295390-G-C		not specified	Uncertain significance (Nov 13, 2024)
11-17295400-C-G		not specified	Uncertain significance (May 26, 2024)
11-17295437-C-A		not specified	Likely benign (May 13, 2022)
11-17295451-C-A		not specified	Uncertain significance (Aug 10, 2024)
11-17295451-C-T		not specified	Uncertain significance (Jun 28, 2024)
11-17296146-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-17301814-G-A		not specified	Uncertain significance (May 25, 2022)
11-17309636-C-G		not specified	Uncertain significance (Nov 23, 2024)
11-17309663-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-17309673-G-A		not specified	Uncertain significance (Mar 27, 2023)
11-17309674-C-T		not specified	Uncertain significance (Dec 23, 2024)
11-17310880-A-G		not specified	Uncertain significance (Jan 31, 2022)
11-17310909-G-C		not specified	Uncertain significance (Feb 25, 2025)
11-17310963-G-C		not specified	Uncertain significance (Jan 08, 2025)
11-17310978-A-G		not specified	Uncertain significance (Jun 22, 2024)
11-17311258-C-A		not specified	Uncertain significance (Dec 17, 2024)
11-17311873-T-G		not specified	Uncertain significance (Sep 07, 2022)
11-17311874-G-A		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUCB2	protein_coding	protein_coding	ENST00000529010	12	141822

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.00e-10	0.410	124736	0	53	124789	0.000212

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.905	164	200	0.820	0.00000901	2843
Missense in Polyphen		58	72.862	0.79603		1073
Synonymous	0.931	57	66.7	0.855	0.00000297	655
Loss of Function	1.07	18	23.6	0.763	0.00000109	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000229
Ashkenazi Jewish	0.00	0.00
East Asian	0.00107	0.00106
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000208	0.000203
Middle Eastern	0.00107	0.00106
South Asian	0.000171	0.000163
Other	0.000193	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-binding protein. May have a role in calcium homeostasis.

Recessive Scores

• pRec: 0.0981

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.319
• hipred: N
• hipred_score: 0.230
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	High	Medium	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Nucb2
• Phenotype: homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of appetite
• Cellular component: extracellular space;nuclear outer membrane;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cytosol;plasma membrane;extracellular exosome
• Molecular function: DNA binding;calcium ion binding;protein binding