ITGA1

protein-coding

integrin subunit alpha 1, the group of Integrin alpha subunits|CD molecules

Gene summary

This gene encodes the alpha 1 subunit of integrin receptors. This protein heterodimerizes with the beta 1 subunit to form a cell-surface receptor for collagen and laminin. The heterodimeric receptor is involved in cell-cell adhesion and may play a role in inflammation and fibrosis. The alpha 1 subunit contains an inserted (I) von Willebrand factor type I domain which is thought to be involved in collagen binding. [provided by RefSeq, Jul 2008]

MANE transcript

NM_181501.2

Inheritance

—

ClinVar variants

U:153B:12

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr5:52,787,916-52,959,209

External References & Databases

Ensembl (ENSG00000213949)

Transcript & Mutation Effects

hg38 • Region Span ~171.3 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 ITGA1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 202

not providedTotal: 11

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181501.2. 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			1 clinvar	3 clinvar	4 clinvar	8
missense			151 clinvar	3 clinvar	2 clinvar	156
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	153	6	6	165

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_181501.2	RefSeq	NP_852478.1	29	MANE Select
ENST00000282588.7	Ensembl	ENSP00000282588.5	29	MANE Select
ENST00000650673.1	Ensembl	ENSP00000498529.1	8	Standard
ENST00000993159.1	Ensembl	ENSP00000662976.1	28	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

PI3K-Akt signaling pathway - Homo sapiens (human)
ECM-receptor interaction - Homo sapiens (human)
Focal adhesion - Homo sapiens (human)
Dilated cardiomyopathy (DCM) - Homo sapiens (human)
Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human)

Biological Process

activation of MAPK activity
muscle contraction
cell-matrix adhesion
integrin-mediated signaling pathway
negative regulation of cell population proliferation

Molecular Function

signaling receptor binding
protein binding
collagen binding
protein phosphatase binding
metal ion binding

Cellular Component

acrosomal vesicle
plasma membrane
focal adhesion
integrin complex
external side of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000282588
Coding exons: 29
Length: 171311
Individuals with no LoFs: 125673
Homozygous LoFs: 0
Heterozygous LoFs: 74
Defined: 125747
p: 0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.981	548	617	0.889	0.0000307	7707
Missense (PolyPhen)		160	214.64	0.74543		2696
Synonymous	-0.625	236	224	1.05	0.0000120	2244
Loss of Function	3.27	36	64.3	0.559	0.00000345	798

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00030	0.00029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00034	0.00033	rare
South Asian	0.00039	0.00039	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Integrin alpha-1/beta-1 is a receptor for laminin and collagen. It recognizes the proline-hydroxylated sequence G-F-P-G- E-R in collagen. Involved in anchorage-dependent, negative regulation of EGF-stimulated cell growth. {ECO:0000269|PubMed:15592458}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.416
RVIS EVS: -0.06
RVIS percentile EVS: 48.89

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.458

Gene Damage Prediction

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