ITGAX

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

Basic information

Region (hg38): 16:31355133-31382999

Previous symbols: [ "CD11C" ]

Links

ENSG00000140678 ∙ NCBI:3687 ∙ OMIM:151510 ∙ HGNC:6152 ∙ Uniprot:P20702 ∙ 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 ITGAX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGAX 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				5	1	6
missense			67	7	2	76
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	67	12	3

Variants in ITGAX

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

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

Position	Type	Phenotype	Significance	ClinVar
16-31355937-A-G		not specified	Uncertain significance (Dec 19, 2022)
16-31355946-C-T		not specified	Uncertain significance (Feb 28, 2024)
16-31355950-T-C		not specified	Uncertain significance (Apr 06, 2024)
16-31355958-G-A		not specified	Uncertain significance (Sep 20, 2023)
16-31356641-C-T		not specified	Uncertain significance (Jun 30, 2022)
16-31356669-C-T		not specified	Uncertain significance (Jan 10, 2022)
16-31356698-A-T		not specified	Uncertain significance (Mar 29, 2023)
16-31356716-A-G		not specified	Uncertain significance (Sep 16, 2021)
16-31356723-T-G		not specified	Uncertain significance (Oct 18, 2021)
16-31357043-C-T		not specified	Uncertain significance (May 30, 2023)
16-31357259-G-A		not specified	Uncertain significance (Mar 11, 2022)
16-31357272-A-G		not specified	Uncertain significance (Sep 29, 2023)
16-31357350-C-A		not specified	Uncertain significance (Jan 03, 2024)
16-31357350-C-T		not specified	Uncertain significance (Jan 29, 2024)
16-31359968-G-A		not specified	Likely benign (May 28, 2024)
16-31359992-C-T		not specified	Uncertain significance (Mar 25, 2024)
16-31360315-G-A		not specified	Likely benign (Dec 16, 2023)
16-31360330-C-T		not specified	Uncertain significance (Apr 01, 2024)
16-31360333-A-G		not specified	Uncertain significance (Apr 22, 2022)
16-31360395-G-T		not specified	Uncertain significance (Jun 01, 2023)
16-31361072-G-A		not specified	Uncertain significance (Dec 27, 2023)
16-31361135-C-T		not specified	Likely benign (May 06, 2022)
16-31361865-G-A		not specified	Uncertain significance (Nov 10, 2022)
16-31362094-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-31362159-A-G		not specified	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGAX	protein_coding	protein_coding	ENST00000268296	30	27864

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-15	1.00	125648	0	100	125748	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.553	658	699	0.941	0.0000418	7583
Missense in Polyphen		258	288	0.89585		3158
Synonymous	-0.695	317	302	1.05	0.0000198	2334
Loss of Function	3.39	35	64.4	0.544	0.00000330	667

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000566	0.000566
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000892	0.000870
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000327	0.000325
Middle Eastern	0.000892	0.000870
South Asian	0.000851	0.000850
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Integrin alpha-X/beta-2 is a receptor for fibrinogen. It recognizes the sequence G-P-R in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Integrin-mediated Cell Adhesion;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;TYROBP Causal Network;Interleukin-4 and 13 signaling;Neutrophil degranulation;Integrin cell surface interactions;Extracellular matrix organization;Innate Immune System;Immune System;Integrin;Cell surface interactions at the vascular wall;Hemostasis;ECM proteoglycans;Beta2 integrin cell surface interactions (Consensus)

Intolerance Scores

• loftool: 0.441
• rvis_EVS: -0.92
• rvis_percentile_EVS: 9.84

Haploinsufficiency Scores

• pHI: 0.0986
• hipred: N
• hipred_score: 0.214
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.799

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itgax
• Phenotype: hematopoietic system phenotype; normal phenotype; immune system phenotype

Gene ontology

• Biological process: cell adhesion;integrin-mediated signaling pathway;animal organ morphogenesis;cytokine-mediated signaling pathway;extracellular matrix organization;heterotypic cell-cell adhesion;neutrophil degranulation;leukocyte migration
• Cellular component: plasma membrane;integrin complex;cell surface;membrane;secretory granule membrane;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: protein binding;signaling receptor activity;metal ion binding