ITGAX

protein-coding

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

Gene summary

This gene encodes the integrin alpha X chain protein. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This protein combines with the beta 2 chain (ITGB2) to form a leukocyte-specific integrin referred to as inactivated-C3b (iC3b) receptor 4 (CR4). The alpha X beta 2 complex seems to overlap the properties of the alpha M beta 2 integrin in the adherence of neutrophils and monocytes to stimulated endothelium cells, and in the phagocytosis of complement coated particles. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

Previous symbols:

CD11C

MANE transcript

NM_000887.5

Inheritance

—

ClinVar variants

U:174B:25

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr16:31,355,134-31,382,999

External References & Databases

Ensembl (ENSG00000140678)

Transcript & Mutation Effects

hg38 • Region Span ~27.9 kb

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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 ITGAX variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 174

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000887.5. 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	6 clinvar	1 clinvar	11
missense			165 clinvar	17 clinvar	1 clinvar	183
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	174	23	2	199

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_000887.5	RefSeq	NP_000878.2	30	MANE Select
ENST00000268296.9	Ensembl	ENSP00000268296.5	30	MANE Select
NM_001286375.2	RefSeq	NP_001273304.1	31	Standard
ENST00000562522.2	Ensembl	ENSP00000454623.1	31	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Complement and coagulation cascades - Homo sapiens (human)
Regulation of actin cytoskeleton - Homo sapiens (human)
Tuberculosis - Homo sapiens (human)
Integrin-mediated Cell Adhesion
Focal Adhesion

Biological Process

cell adhesion
integrin-mediated signaling pathway
animal organ morphogenesis
cytokine-mediated signaling pathway
extracellular matrix organization

Molecular Function

protein binding
signaling receptor activity
metal ion binding

Cellular Component

plasma membrane
integrin complex
cell surface
membrane
secretory granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000268296
Coding exons: 30
Length: 27864
Individuals with no LoFs: 125648
Homozygous LoFs: 0
Heterozygous LoFs: 100
Defined: 125748
p: 0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.553	658	699	0.941	0.0000418	7583
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00089	0.00087	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.00085	0.00085	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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.;

Intolerance Scores

LoFtool: 0.441
RVIS EVS: -0.92
RVIS percentile EVS: 9.84

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.799

Gene Damage Prediction

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