ITGA10

integrin subunit alpha 10, the group of Integrin alpha subunits

Basic information

Region (hg38): 1:145891208-145910111

Links

ENSG00000143127 ∙ NCBI:8515 ∙ OMIM:604042 ∙ HGNC:6135 ∙ Uniprot:O75578 ∙ 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 ITGA10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGA10 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				1		1
missense			86	2		88
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	86	3	0

Variants in ITGA10

This is a list of pathogenic ClinVar variants found in the ITGA10 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-145892806-C-T		not specified	Uncertain significance (Apr 09, 2024)
1-145892846-A-C		not specified	Uncertain significance (Aug 11, 2024)
1-145893272-G-C		not specified	Uncertain significance (Sep 06, 2022)
1-145893550-C-T		not specified	Uncertain significance (Sep 14, 2022)
1-145893560-C-T		not specified	Uncertain significance (May 03, 2023)
1-145893563-T-A		not specified	Uncertain significance (Sep 30, 2024)
1-145895337-C-A		not specified	Uncertain significance (Dec 08, 2023)
1-145895645-G-T		not specified	Uncertain significance (Nov 25, 2024)
1-145895668-G-A		not specified	Uncertain significance (Jan 08, 2024)
1-145895710-G-T		not specified	Uncertain significance (Oct 02, 2023)
1-145895994-T-C		not specified	Uncertain significance (Nov 09, 2024)
1-145896051-C-A		not specified	Uncertain significance (Nov 18, 2022)
1-145896068-C-T		not specified	Uncertain significance (Sep 26, 2023)
1-145896335-C-T		not specified	Uncertain significance (Oct 25, 2024)
1-145896800-T-C		not specified	Uncertain significance (Jun 28, 2024)
1-145896844-C-A		not specified	Uncertain significance (Mar 25, 2024)
1-145896844-C-T		not specified	Uncertain significance (Mar 21, 2022)
1-145896850-A-G		not specified	Uncertain significance (Dec 01, 2022)
1-145897026-T-A		not specified	Uncertain significance (Jul 05, 2023)
1-145897048-G-A		not specified	Uncertain significance (May 18, 2023)
1-145897083-G-A		not specified	Uncertain significance (Apr 05, 2023)
1-145897273-G-A		not specified	Uncertain significance (Nov 04, 2023)
1-145897531-A-G		not specified	Uncertain significance (Oct 07, 2024)
1-145897544-T-C		not specified	Uncertain significance (Jan 23, 2024)
1-145897625-G-A		not specified	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGA10	protein_coding	protein_coding	ENST00000369304	30	18978

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.45e-19	0.996	125548	0	200	125748	0.000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.881	587	650	0.903	0.0000355	7475
Missense in Polyphen		210	232.07	0.90489		2764
Synonymous	0.862	232	249	0.931	0.0000121	2475
Loss of Function	3.01	41	67.8	0.605	0.00000410	682

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00209	0.00208
Ashkenazi Jewish	0.00	0.00
East Asian	0.000979	0.000979
Finnish	0.000464	0.000462
European (Non-Finnish)	0.000787	0.000783
Middle Eastern	0.000979	0.000979
South Asian	0.000723	0.000686
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Integrin alpha-10/beta-1 is a receptor for collagen.
• Pathway: 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);Regulation of actin cytoskeleton - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Integrin-mediated Cell Adhesion;Arrhythmogenic Right Ventricular Cardiomyopathy;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Developmental Biology;Integrin cell surface interactions;Extracellular matrix organization;Platelet Adhesion to exposed collagen;Integrin;CHL1 interactions;Hemostasis;Arf6 trafficking events;L1CAM interactions;Plexin-D1 Signaling;Axon guidance;Beta1 integrin cell surface interactions (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.788
• rvis_EVS: 1.27
• rvis_percentile_EVS: 93.67

Haploinsufficiency Scores

• pHI: 0.539
• hipred: N
• hipred_score: 0.422
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.651

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itga10
• Phenotype: skeleton phenotype; limbs/digits/tail phenotype

Zebrafish Information Network

• Gene name: itga10
• Affected structure: skeletal tissue
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: cell-matrix adhesion;integrin-mediated signaling pathway;extracellular matrix organization
• Cellular component: plasma membrane;integrin complex;integrin alpha10-beta1 complex
• Molecular function: collagen binding;metal ion binding;collagen binding involved in cell-matrix adhesion