CD33

CD33 molecule, the group of V-set domain containing|CD molecules|Sialic acid binding Ig like lectins

Basic information

Region (hg38): 19:51225064-51243860

Links

ENSG00000105383 ∙ NCBI:945 ∙ OMIM:159590 ∙ HGNC:1659 ∙ Uniprot:P20138 ∙ 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 CD33 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD33 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	1	3
missense			17	4	10	31
nonsense						0
start loss			1			1
frameshift				1	1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					4	4
Total	0	0	18	7	16

Variants in CD33

This is a list of pathogenic ClinVar variants found in the CD33 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-51225119-A-G			Uncertain significance (Sep 01, 2017)
19-51225219-G-A			Benign (Jul 31, 2018)
19-51225221-C-T			Benign (Aug 22, 2019)
19-51225256-C-G		not specified	Uncertain significance (Jan 29, 2024)
19-51225269-C-T		not specified	Uncertain significance (May 12, 2024)
19-51225289-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-51225311-T-C			Benign (Jul 16, 2018)
19-51225317-C-CCATAAA		CD33-related disorder	Uncertain significance (Jul 15, 2024)
19-51225331-G-A		not specified	Uncertain significance (Sep 27, 2022)
19-51225344-C-T		not specified	Uncertain significance (Dec 08, 2023)
19-51225361-T-C		not specified	Uncertain significance (Oct 26, 2022)
19-51225365-G-A		CD33-related disorder	Likely benign (Jun 05, 2018)
19-51225373-G-C			Benign (Dec 13, 2017)
19-51225385-A-G			Benign (Aug 22, 2019)
19-51225451-C-T		not specified	Uncertain significance (Dec 13, 2022)
19-51225502-G-A		not specified	Uncertain significance (Mar 11, 2022)
19-51225517-A-G		not specified	Uncertain significance (Feb 17, 2024)
19-51225530-T-A		not specified	Uncertain significance (Dec 19, 2023)
19-51225535-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-51225559-T-C			Likely benign (Jan 01, 2023)
19-51225563-G-A			Benign (May 15, 2018)
19-51225590-A-G			Benign (May 15, 2018)
19-51225806-T-C		not specified	Uncertain significance (Dec 27, 2023)
19-51225839-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-51225847-CCCGG-C		CD33-related disorder	Benign (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD33	protein_coding	protein_coding	ENST00000262262	7	18796

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.69e-7	0.441	121860	57	3831	125748	0.0156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.141	211	205	1.03	0.0000109	2328
Missense in Polyphen		43	46.914	0.91657		583
Synonymous	0.540	81	87.4	0.927	0.00000515	768
Loss of Function	0.698	11	13.8	0.797	5.87e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0356	0.0346
Ashkenazi Jewish	0.00120	0.00119
East Asian	0.000275	0.000272
Finnish	0.00361	0.00361
European (Non-Finnish)	0.0250	0.0249
Middle Eastern	0.000275	0.000272
South Asian	0.00124	0.00121
Other	0.0189	0.0186

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative adhesion molecule of myelomonocytic-derived cells that mediates sialic-acid dependent binding to cells. Preferentially binds to alpha-2,6-linked sialic acid. The sialic acid recognition site may be masked by cis interactions with sialic acids on the same cell surface. In the immune response, may act as an inhibitory receptor upon ligand induced tyrosine phosphorylation by recruiting cytoplasmic phosphatase(s) via their SH2 domain(s) that block signal transduction through dephosphorylation of signaling molecules. Induces apoptosis in acute myeloid leukemia (in vitro). {ECO:0000269|PubMed:10556798, ECO:0000269|PubMed:11320212}.
• Pathway: Hematopoietic cell lineage - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.0812

Intolerance Scores

• loftool: 0.981
• rvis_EVS: 2.29
• rvis_percentile_EVS: 98.31

Haploinsufficiency Scores

• pHI: 0.0350
• hipred: N
• hipred_score: 0.166
• ghis: 0.388

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0558

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd33
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: immune response-inhibiting signal transduction;cell adhesion;signal transduction;cell-cell signaling;negative regulation of cell population proliferation;neutrophil degranulation;regulation of immune response
• Cellular component: nucleus;plasma membrane;integral component of plasma membrane;external side of plasma membrane;specific granule membrane;tertiary granule membrane
• Molecular function: protein binding;protein phosphatase binding;carbohydrate binding;signaling receptor activity