ITGAM

integrin subunit alpha M, the group of CD molecules|Integrin alpha subunits|Complement system regulators and receptors

Basic information

Region (hg38): 16:31259967-31332892

Previous symbols: [ "CR3A", "CD11B" ]

Links

ENSG00000169896 ∙ NCBI:3684 ∙ OMIM:120980 ∙ HGNC:6149 ∙ Uniprot:P11215 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• systemic lupus erythematosus (Supportive), mode of inheritance: Unknown

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGAM 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	157	9	168
missense			406	19	10	435
nonsense			10	3		13
start loss						0
frameshift			12			12
inframe indel			3			3
splice donor/acceptor (+/-2bp)			8			8
splice region			26	45	1	72
non coding			11	126	10	147
Total	0	0	452	305	29

Variants in ITGAM

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

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

Position	Type	Phenotype	Significance	ClinVar
16-31260068-G-T			Uncertain significance (Jan 06, 2024)
16-31260071-C-T			Uncertain significance (Oct 26, 2023)
16-31260072-T-G			Uncertain significance (Jul 21, 2024)
16-31260078-T-C			Uncertain significance (Nov 23, 2021)
16-31260079-C-G			Likely benign (Nov 11, 2023)
16-31260097-A-C			Uncertain significance (May 27, 2024)
16-31260099-G-A			Likely benign (Nov 08, 2022)
16-31260105-G-C			Likely benign (Apr 14, 2021)
16-31260106-G-GCAC			Likely benign (Sep 27, 2022)
16-31260109-T-A			Likely benign (Jan 26, 2024)
16-31261679-A-C			Likely benign (May 13, 2024)
16-31261686-C-T			Likely benign (Jan 07, 2025)
16-31261693-C-T			Likely benign (Mar 18, 2024)
16-31261718-T-C			Likely benign (Oct 24, 2024)
16-31261721-G-A			Uncertain significance (Jun 15, 2022)
16-31261722-A-G			Uncertain significance (Dec 24, 2023)
16-31261725-C-T			Uncertain significance (Oct 22, 2023)
16-31261732-C-T			Likely benign (Oct 13, 2023)
16-31261753-C-T			Likely benign (Dec 30, 2023)
16-31261754-G-A		not specified	Uncertain significance (Nov 25, 2024)
16-31261759-G-A			Likely benign (Feb 10, 2022)
16-31261761-G-A			Uncertain significance (Aug 28, 2024)
16-31261765-C-T			Likely benign (Oct 23, 2024)
16-31261766-G-A			Uncertain significance (Jul 11, 2022)
16-31261774-C-T			Likely benign (Aug 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGAM	protein_coding	protein_coding	ENST00000544665	30	72903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.31e-11	1.00	125406	0	152	125558	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	582	687	0.847	0.0000410	7488
Missense in Polyphen		207	273.92	0.75568		3135
Synonymous	1.04	262	284	0.922	0.0000179	2287
Loss of Function	3.87	28	60.5	0.463	0.00000305	677

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000642	0.000610
Ashkenazi Jewish	0.00427	0.00408
East Asian	0.000398	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000635	0.000625
Middle Eastern	0.000398	0.000381
South Asian	0.000566	0.000555
Other	0.000501	0.000491

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Integrin ITGAM/ITGB2 is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is identical with CR-3, the receptor for the iC3b fragment of the third complement component. It probably recognizes the R-G-D peptide in C3b. Integrin ITGAM/ITGB2 is also a receptor for fibrinogen, factor X and ICAM1. It recognizes P1 and P2 peptides of fibrinogen gamma chain. Regulates neutrophil migration (PubMed:28807980). In association with beta subunit ITGB2/CD18, required for CD177-PRTN3-mediated activation of TNF primed neutrophils (PubMed:21193407). May regulate phagocytosis-induced apoptosis in extravasated neutrophils (By similarity). May play a role in mast cell development (By similarity). {ECO:0000250|UniProtKB:P05555, ECO:0000269|PubMed:21193407, ECO:0000269|PubMed:28807980, ECO:0000305}.
• Disease: DISEASE: Systemic lupus erythematosus 6 (SLEB6) [MIM:609939]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269|PubMed:18204446, ECO:0000269|PubMed:18204448}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Cell adhesion molecules (CAMs) - Homo sapiens (human);Pertussis - Homo sapiens (human);Legionellosis - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);Phagosome - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Staphylococcus aureus infection - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Integrin-mediated Cell Adhesion;Vitamin D Receptor Pathway;Focal Adhesion;Microglia Pathogen Phagocytosis Pathway;TYROBP Causal Network;Interleukin-4 and 13 signaling;Fibrin Complement Receptor 3 Signaling Pathway;Neutrophil degranulation;Integrin cell surface interactions;Toll-Like Receptors Cascades;Extracellular matrix organization;Innate Immune System;Immune System;Integrin;Cell surface interactions at the vascular wall;Hemostasis;Toll Like Receptor 4 (TLR4) Cascade;amb2 Integrin signaling;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;Beta2 integrin cell surface interactions (Consensus)

Intolerance Scores

• loftool: 0.543
• rvis_EVS: -0.59
• rvis_percentile_EVS: 18.28

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.474
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.562

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itgam
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; immune 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); hematopoietic system phenotype

Gene ontology

• Biological process: microglial cell activation;phagocytosis, engulfment;cell adhesion;integrin-mediated signaling pathway;ectodermal cell differentiation;cytokine-mediated signaling pathway;extracellular matrix organization;positive regulation of superoxide anion generation;toll-like receptor 4 signaling pathway;neutrophil degranulation;positive regulation of neutrophil degranulation;innate immune response;negative regulation of dopamine metabolic process;leukocyte migration;positive regulation of phagocytosis, engulfment;positive regulation of protein targeting to membrane;amyloid-beta clearance;cell-cell adhesion via plasma-membrane adhesion molecules;complement-mediated synapse pruning;vertebrate eye-specific patterning;positive regulation of neuron death;positive regulation of microglial cell activation;cell surface receptor signaling pathway involved in cell-cell signaling;positive regulation of prostaglandin-E synthase activity
• Cellular component: extracellular space;plasma membrane;integrin complex;external side of plasma membrane;cell surface;integrin alphaM-beta2 complex;specific granule membrane;plasma membrane raft;extracellular exosome;tertiary granule membrane
• Molecular function: amyloid-beta binding;complement component C3b binding;protein binding;heat shock protein binding;metal ion binding;protein heterodimerization activity