CD33

protein-coding

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

Gene summary

Enables protein phosphatase binding activity; protein tyrosine phosphatase activator activity; and sialic acid binding activity. Involved in several processes, including immune response-regulating signaling pathway; negative regulation of cytokine production; and negative regulation of monocyte activation. Located in Golgi apparatus; external side of plasma membrane; and peroxisome. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001772.4

Inheritance

—

ClinVar variants

U:43B:20

Top phenotype

CD33-related disorder

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr19:51,225,064-51,243,860

External References & Databases

Ensembl (ENSG00000105383)

Transcript & Mutation Effects

hg38 • Region Span ~18.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CD33 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 15

CD33-related disorderTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001772.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	2 clinvar	2 clinvar	8
missense			38 clinvar	8 clinvar	6 clinvar	52
nonsense						0
start loss			1 clinvar			1
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)					1 clinvar	1
Total	0	0	43	11	9	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001772.4	RefSeq	NP_001763.3	7	MANE Select
ENST00000262262.5	Ensembl	ENSP00000262262.3	7	MANE Select
NM_001082618.2	RefSeq	NP_001076087.1	6	Standard
NM_001177608.2	RefSeq	NP_001171079.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Hematopoietic cell lineage - Homo sapiens (human)
Neutrophil degranulation
Innate Immune System
Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell

Biological Process

immune response-inhibiting signal transduction
cell adhesion
signal transduction
cell-cell signaling
negative regulation of cell population proliferation

Molecular Function

protein binding
protein phosphatase binding
carbohydrate binding
signaling receptor activity

Cellular Component

nucleus
plasma membrane
integral component of plasma membrane
external side of plasma membrane
specific granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262262
Coding exons: 7
Length: 18796
Individuals with no LoFs: 121860
Homozygous LoFs: 57
Heterozygous LoFs: 3831
Defined: 125748
p: 0.0156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.141	211	205	1.03	0.0000109	2328
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.020	0.019	notable
Latino/Admixed American	0.016	0.016	notable
Ashkenazi Jewish	0.0012	0.0012	notable
East Asian	0.00027	0.00027	rare
Finnish	0.0036	0.0036	notable
European (Non-Finnish)	0.025	0.025	notable
South Asian	0.0012	0.0012	notable
Other	0.019	0.019	notable

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0812

Intolerance Scores

LoFtool: 0.981
RVIS EVS: 2.29
RVIS percentile EVS: 98.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0558

Gene Damage Prediction

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