CD22

CD22 molecule, the group of CD molecules|C2-set domain containing|Sialic acid binding Ig like lectins|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:35319260-35347361

Links

ENSG00000012124 ∙ NCBI:933 ∙ OMIM:107266 ∙ HGNC:1643 ∙ Uniprot:P20273 ∙ 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 CD22 gene.

• Inborn genetic diseases (40 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD22 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				1	2	3
missense			37	6	2	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1			1
Total	0	0	38	7	4

Variants in CD22

This is a list of pathogenic ClinVar variants found in the CD22 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35332053-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-35332604-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-35332629-C-T			Likely benign (Feb 01, 2023)
19-35332718-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-35332801-G-T		not specified	Uncertain significance (Nov 29, 2021)
19-35336068-C-T		not specified	Uncertain significance (Apr 28, 2023)
19-35336078-A-G		not specified	Likely benign (Jun 09, 2022)
19-35336135-C-T		not specified	Uncertain significance (Feb 09, 2022)
19-35336188-A-G		not specified	Uncertain significance (Aug 17, 2022)
19-35336192-C-T		not specified	Likely benign (Mar 07, 2023)
19-35336228-G-A		not specified	Uncertain significance (Nov 01, 2022)
19-35336229-C-A		not specified	Uncertain significance (Mar 07, 2024)
19-35336236-A-C		not specified	Uncertain significance (Nov 09, 2022)
19-35336272-G-A		not specified	Uncertain significance (Oct 25, 2023)
19-35336279-G-T		not specified	Uncertain significance (Sep 22, 2023)
19-35337831-C-T			Benign (Mar 29, 2018)
19-35337832-G-A		not specified	Likely benign (Jun 07, 2023)
19-35337835-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-35337923-T-A		not specified	Uncertain significance (Jan 27, 2022)
19-35337928-G-A			Uncertain significance (Mar 30, 2021)
19-35337940-G-A		not specified	Uncertain significance (Jul 31, 2023)
19-35338003-G-A		not specified	Uncertain significance (Nov 01, 2021)
19-35338020-G-C		not specified	Uncertain significance (Jan 27, 2022)
19-35338207-C-T		not specified	Uncertain significance (Mar 21, 2023)
19-35338255-A-G		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD22	protein_coding	protein_coding	ENST00000085219	13	28095

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.804	0.196	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.674	445	487	0.914	0.0000278	5555
Missense in Polyphen		95	131.83	0.72064		1552
Synonymous	-0.332	214	208	1.03	0.0000136	1630
Loss of Function	4.97	9	45.0	0.200	0.00000255	445

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.0000972	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates B-cell B-cell interactions. May be involved in the localization of B-cells in lymphoid tissues. Binds sialylated glycoproteins; one of which is CD45. Preferentially binds to alpha-2,6-linked sialic acid. The sialic acid recognition site can be masked by cis interactions with sialic acids on the same cell surface. Upon ligand induced tyrosine phosphorylation in the immune response seems to be involved in regulation of B-cell antigen receptor signaling. Plays a role in positive regulation through interaction with Src family tyrosine kinases and may also act as an inhibitory receptor by recruiting cytoplasmic phosphatases via their SH2 domains that block signal transduction through dephosphorylation of signaling molecules.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);B cell receptor signaling pathway - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);B Cell Receptor Signaling Pathway;Antigen activates B Cell Receptor (BCR) leading to generation of second messengers;Signaling by the B Cell Receptor (BCR);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;CD22 mediated BCR regulation;BCR;BCR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.282

Intolerance Scores

• loftool: 0.238
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.95

Haploinsufficiency Scores

• pHI: 0.368
• hipred: N
• hipred_score: 0.371
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.402

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd22
• Phenotype: cellular 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); hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cell adhesion;regulation of endocytosis;regulation of B cell proliferation;regulation of immune response;negative regulation of calcium-mediated signaling;negative regulation of B cell receptor signaling pathway;negative regulation of immunoglobulin secretion
• Cellular component: cytoplasm;early endosome;plasma membrane;cell surface;integral component of membrane;neuronal cell body membrane;recycling endosome;extracellular exosome
• Molecular function: IgM binding;signaling receptor binding;protein binding;protein phosphatase binding;carbohydrate binding;sialic acid binding;CD4 receptor binding