VPREB1

V-set pre-B cell surrogate light chain 1, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 22:22244780-22245515

Links

ENSG00000169575 ∙ NCBI:7441 ∙ OMIM:605141 ∙ HGNC:12709 ∙ Uniprot:P12018 ∙ 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 VPREB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPREB1 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in VPREB1

This is a list of pathogenic ClinVar variants found in the VPREB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-22244826-C-G		not specified	Uncertain significance (Jun 10, 2024)
22-22244966-C-G		not specified	Uncertain significance (Jan 23, 2024)
22-22244979-C-T		not specified	Uncertain significance (Apr 20, 2024)
22-22245059-G-A		not specified	Likely benign (Feb 13, 2024)
22-22245152-C-T		not specified	Uncertain significance (Mar 31, 2023)
22-22245173-G-A		not specified	Uncertain significance (Aug 17, 2021)
22-22245195-A-T		not specified	Uncertain significance (Nov 08, 2022)
22-22245204-T-A		not specified	Uncertain significance (Feb 23, 2023)
22-22245254-G-T		not specified	Uncertain significance (Jan 29, 2024)
22-22245266-G-C		not specified	Uncertain significance (Feb 06, 2023)
22-22245287-G-C		not specified	Uncertain significance (Mar 12, 2024)
22-22245326-C-T		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPREB1	protein_coding	protein_coding	ENST00000403807	2	841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0965	0.593	125665	0	4	125669	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.127	81	84.3	0.961	0.00000480	919
Missense in Polyphen		26	27.856	0.93338		319
Synonymous	-0.253	37	35.1	1.05	0.00000237	279
Loss of Function	0.0928	1	1.11	0.905	4.70e-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	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
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. This complex presumably regulates Ig gene rearrangements in the early steps of B-cell differentiation.
• Pathway: Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.267

Intolerance Scores

• loftool: 0.625
• rvis_EVS: 0.68
• rvis_percentile_EVS: 85.04

Haploinsufficiency Scores

• pHI: 0.0230
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.133

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vpreb1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

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