VPREB3

V-set pre-B cell surrogate light chain 3, the group of V-set domain containing

Basic information

Region (hg38): 22:23752743-23754425

Links

ENSG00000128218 ∙ NCBI:29802 ∙ OMIM:605017 ∙ HGNC:12710 ∙ Uniprot:Q9UKI3 ∙ 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 VPREB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPREB3 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in VPREB3

This is a list of pathogenic ClinVar variants found in the VPREB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-23752890-C-T		not specified	Likely benign (Jun 05, 2024)
22-23752916-G-A		not specified	Uncertain significance (Sep 06, 2022)
22-23752916-G-T		not specified	Uncertain significance (Jan 23, 2024)
22-23752920-C-T		not specified	Uncertain significance (Dec 30, 2023)
22-23752950-G-T		not specified	Uncertain significance (Jun 27, 2023)
22-23752985-G-A		not specified	Uncertain significance (Feb 13, 2024)
22-23752995-C-T		not specified	Uncertain significance (Aug 30, 2021)
22-23753069-C-T		not specified	Uncertain significance (Aug 29, 2022)
22-23753074-C-G		not specified	Uncertain significance (Aug 20, 2023)
22-23753075-T-C		not specified	Uncertain significance (Jul 19, 2022)
22-23753091-C-T		not specified	Uncertain significance (Sep 16, 2021)
22-23753105-G-T		not specified	Uncertain significance (Jul 07, 2022)
22-23753111-T-G		not specified	Uncertain significance (Apr 01, 2024)
22-23753114-T-C		not specified	Likely benign (Jun 06, 2023)
22-23753119-G-T		not specified	Uncertain significance (Feb 21, 2024)
22-23753168-G-A		not specified	Uncertain significance (May 17, 2023)
22-23754353-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPREB3	protein_coding	protein_coding	ENST00000248948	2	1726

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0946	0.590	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.285	83	76.0	1.09	0.00000484	778
Missense in Polyphen		35	24.64	1.4205		244
Synonymous	-0.729	41	35.5	1.16	0.00000257	255
Loss of Function	0.0592	1	1.07	0.938	4.54e-8	12

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with the Ig-mu chain to form a molecular complex that is expressed on the surface of pre-B-cells.
• Pathway: Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.182

Intolerance Scores

• loftool: 0.711
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.146
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vpreb3

Gene ontology

• Biological process: immunoglobulin production;immune response;leukocyte migration
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum