CD19

CD19 molecule, the group of CD molecules|Minor histocompatibility antigens|Immunoglobulin like domain containing

Basic information

Region (hg38): 16:28931965-28939342

Links

ENSG00000177455 ∙ NCBI:930 ∙ OMIM:107265 ∙ HGNC:1633 ∙ Uniprot:P15391 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• common variable immunodeficiency (Supportive), mode of inheritance: AD
• immunodeficiency, common variable, 3 (Strong), mode of inheritance: AR
• immunodeficiency, common variable, 3 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency, common variable 3	AR	Allergy/Immunology/Infectious	Indidivuals may demonstrate increased susceptibility to infections, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious	16672701

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD19 gene.

• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD19 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			2	81	2	85
missense		1	128	2	2	133
nonsense	1	1				2
start loss						0
frameshift	2		2			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)		3		1		4
splice region			8	12		20
non coding			13	44	9	66
Total	3	5	146	128	13

Variants in CD19

This is a list of pathogenic ClinVar variants found in the CD19 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28931985-G-A		Immunodeficiency, common variable, 3	Uncertain significance (Jan 13, 2018)
16-28932013-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (May 23, 2023)
16-28932014-G-A		Inborn genetic diseases	Uncertain significance (Dec 11, 2023)
16-28932017-T-G		Immunodeficiency, common variable, 3	Uncertain significance (Jan 13, 2018)
16-28932024-C-A		Immunodeficiency, common variable, 3	Uncertain significance (Jun 28, 2021)
16-28932030-C-T			Benign (Sep 04, 2023)
16-28932031-C-T			Uncertain significance (Aug 04, 2023)
16-28932042-C-T			Likely benign (Aug 09, 2021)
16-28932047-T-C		Immunodeficiency, common variable, 3	Likely benign (May 21, 2020)
16-28932060-C-T			Likely benign (Aug 30, 2022)
16-28932061-G-C		Immunodeficiency, common variable, 3	Uncertain significance (Feb 08, 2022)
16-28932069-T-G			Likely benign (Apr 30, 2023)
16-28932085-G-C		Immunodeficiency, common variable, 3	Uncertain significance (May 20, 2023)
16-28932102-G-A			Likely benign (Mar 12, 2023)
16-28932333-T-TCTCTCTCCAC			Likely benign (Jun 21, 2022)
16-28932351-G-A			Uncertain significance (Jul 14, 2022)
16-28932356-C-T			Likely benign (Aug 27, 2021)
16-28932360-G-A			Uncertain significance (Dec 23, 2023)
16-28932365-G-A			Likely benign (Jul 05, 2022)
16-28932376-A-G			Uncertain significance (May 15, 2022)
16-28932385-C-A			Pathogenic (Jun 29, 2021)
16-28932387-G-T		Inborn genetic diseases	Uncertain significance (Feb 10, 2023)
16-28932397-C-A			Uncertain significance (Feb 25, 2022)
16-28932397-C-T		Inborn genetic diseases	Uncertain significance (Dec 09, 2023)
16-28932404-G-A		Immunodeficiency, common variable, 3 • CD19-related disorder	Conflicting classifications of pathogenicity (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD19	protein_coding	protein_coding	ENST00000538922	14	7408

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.905	0.0950	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	270	322	0.839	0.0000191	3571
Missense in Polyphen		124	150.04	0.82645		1639
Synonymous	-0.217	138	135	1.02	0.00000856	1137
Loss of Function	4.19	5	29.6	0.169	0.00000134	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Assembles with the antigen receptor of B-lymphocytes in order to decrease the threshold for antigen receptor-dependent stimulation.
• Disease: DISEASE: Immunodeficiency, common variable, 3 (CVID3) [MIM:613493]: A primary immunodeficiency characterized by antibody deficiency, hypogammaglobulinemia, recurrent bacterial infections and an inability to mount an antibody response to antigen. The defect results from a failure of B-cell differentiation and impaired secretion of immunoglobulins; the numbers of circulating B-cells is usually in the normal range, but can be low. {ECO:0000269|PubMed:16672701}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Primary immunodeficiency - Homo sapiens (human);B cell receptor signaling pathway - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);B Cell Receptor Signaling Pathway;Human Complement System;PI3K-Akt Signaling Pathway;Antigen activates B Cell Receptor (BCR) leading to generation of second messengers;Disease;Signal Transduction;B cell receptor signaling;Signaling by the B Cell Receptor (BCR);Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;BCR;BCR signaling pathway;PIP3 activates AKT signaling;Regulation of Complement cascade;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Complement cascade;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K/AKT Signaling in Cancer;Intracellular signaling by second messengers;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.517

Intolerance Scores

• loftool: 0.411
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.754
• hipred: Y
• hipred_score: 0.504
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd19
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular 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); hematopoietic system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; immune system phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: cellular defense response;cell surface receptor signaling pathway;regulation of complement activation;phosphatidylinositol phosphorylation;regulation of immune response;B cell receptor signaling pathway;positive regulation of release of sequestered calcium ion into cytosol;positive regulation of protein kinase B signaling
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;protein-containing complex;extracellular exosome
• Molecular function: protein binding;phosphatidylinositol-4,5-bisphosphate 3-kinase activity