NUCB1

nucleobindin 1, the group of EF-hand domain containing

Basic information

Region (hg38): 19:48900050-48923473

Links

ENSG00000104805 ∙ NCBI:4924 ∙ OMIM:601323 ∙ HGNC:8043 ∙ Uniprot:Q02818 ∙ 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 NUCB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUCB1 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in NUCB1

This is a list of pathogenic ClinVar variants found in the NUCB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48900822-C-T		not specified	Uncertain significance (Nov 27, 2023)
19-48900825-T-C		not specified	Uncertain significance (Apr 22, 2024)
19-48900870-T-C		not specified	Uncertain significance (Apr 26, 2023)
19-48900890-G-C		not specified	Uncertain significance (Sep 07, 2022)
19-48904357-T-G		not specified	Uncertain significance (Mar 11, 2024)
19-48904369-G-A		not specified	Uncertain significance (May 27, 2022)
19-48905780-T-A		not specified	Uncertain significance (Apr 25, 2022)
19-48905796-T-A		not specified	Uncertain significance (Dec 16, 2023)
19-48905810-G-T		not specified	Uncertain significance (Jan 25, 2023)
19-48905838-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-48911185-T-C		not specified	Uncertain significance (Sep 16, 2021)
19-48913027-C-T		not specified	Uncertain significance (Jul 20, 2021)
19-48913092-C-T		not specified	Uncertain significance (Jul 08, 2022)
19-48913093-G-A		not specified	Uncertain significance (Oct 13, 2023)
19-48913096-G-A		not specified	Uncertain significance (May 10, 2022)
19-48913162-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-48913170-C-T		not specified	Uncertain significance (Apr 24, 2024)
19-48913496-A-C		not specified	Uncertain significance (Jun 21, 2023)
19-48913556-T-C		not specified	Uncertain significance (Mar 21, 2022)
19-48918728-A-G		not specified	Uncertain significance (Nov 30, 2022)
19-48919051-A-C		not specified	Uncertain significance (Oct 06, 2022)
19-48919086-G-T		not specified	Uncertain significance (Oct 27, 2023)
19-48919235-C-G		not specified	Uncertain significance (Oct 06, 2022)
19-48919250-G-T		not specified	Uncertain significance (Sep 27, 2021)
19-48921157-G-T		not specified	Uncertain significance (May 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUCB1	protein_coding	protein_coding	ENST00000405315	12	23323

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.16e-8	0.978	125700	0	47	125747	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.933	251	296	0.847	0.0000192	3011
Missense in Polyphen		68	87.033	0.78132		897
Synonymous	0.659	111	120	0.923	0.00000727	892
Loss of Function	2.17	16	28.5	0.561	0.00000162	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000594	0.000590
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000230	0.000220
Middle Eastern	0.00	0.00
South Asian	0.000138	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major calcium-binding protein of the Golgi. May have a role in calcium homeostasis (By similarity). {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.232

Intolerance Scores

• loftool: 0.632
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.43

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.484
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nucb1

Gene ontology

• Biological process: post-translational protein modification;cellular protein metabolic process;response to cisplatin;regulation of protein targeting
• Cellular component: extracellular space;nucleus;early endosome;endoplasmic reticulum lumen;rough endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;Golgi-associated vesicle;cis-Golgi network;trans-Golgi network;membrane;Golgi cisterna membrane;extracellular exosome;extrinsic component of Golgi membrane;lumenal side of Golgi membrane
• Molecular function: G-protein alpha-subunit binding;DNA binding;calcium ion binding;protein binding