ITGAD

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

Basic information

Region (hg38): 16:31393335-31426505

Links

ENSG00000156886 ∙ NCBI:3681 ∙ OMIM:602453 ∙ HGNC:6146 ∙ Uniprot:Q13349 ∙ 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 ITGAD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGAD 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			77	8		85
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	77	9	0

Variants in ITGAD

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

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

Position	Type	Phenotype	Significance	ClinVar
16-31394281-C-T		not specified	Uncertain significance (Oct 17, 2023)
16-31394318-C-A		not specified	Uncertain significance (Nov 10, 2022)
16-31394331-G-A		not specified	Uncertain significance (Feb 14, 2023)
16-31397372-G-A		not specified	Uncertain significance (Jul 25, 2023)
16-31397375-C-A		not specified	Uncertain significance (May 31, 2023)
16-31397403-C-T		not specified	Uncertain significance (Apr 11, 2023)
16-31397409-G-A		not specified	Uncertain significance (Oct 25, 2023)
16-31397454-C-T		not specified	Uncertain significance (May 09, 2024)
16-31397650-A-G		not specified	Uncertain significance (Jun 16, 2024)
16-31397659-G-A		not specified	Uncertain significance (Jan 17, 2023)
16-31397845-G-C		not specified	Uncertain significance (Mar 02, 2023)
16-31397852-T-G		not specified	Uncertain significance (Oct 03, 2023)
16-31397868-C-T		not specified	Uncertain significance (Nov 08, 2021)
16-31397900-G-A		not specified	Uncertain significance (Oct 25, 2022)
16-31397906-C-T		not specified	Uncertain significance (Dec 14, 2023)
16-31402136-A-C		not specified	Uncertain significance (Mar 11, 2022)
16-31402216-A-G		not specified	Uncertain significance (Nov 17, 2022)
16-31403585-T-C		not specified	Uncertain significance (Mar 30, 2022)
16-31403627-C-T		not specified	Uncertain significance (Jul 20, 2022)
16-31407547-G-A		not specified	Uncertain significance (Dec 15, 2022)
16-31407571-T-C		not specified	Uncertain significance (Jul 09, 2021)
16-31407820-T-C		not specified	Uncertain significance (Jan 08, 2024)
16-31407830-C-T		not specified	Uncertain significance (Apr 25, 2022)
16-31407841-G-A		not specified	Uncertain significance (Mar 27, 2023)
16-31407899-A-G		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGAD	protein_coding	protein_coding	ENST00000389202	30	33194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.00e-21	0.891	125113	1	634	125748	0.00253

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.850	628	691	0.909	0.0000404	7560
Missense in Polyphen		180	201.27	0.89433		2241
Synonymous	-1.02	315	293	1.08	0.0000190	2343
Loss of Function	2.44	43	64.0	0.672	0.00000330	676

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00519	0.00513
Ashkenazi Jewish	0.000893	0.000893
East Asian	0.00229	0.00229
Finnish	0.00146	0.00143
European (Non-Finnish)	0.00322	0.00311
Middle Eastern	0.00229	0.00229
South Asian	0.00218	0.00216
Other	0.00303	0.00294

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Integrin alpha-D/beta-2 is a receptor for ICAM3 and VCAM1. May play a role in the atherosclerotic process such as clearing lipoproteins from plaques and in phagocytosis of blood- borne pathogens, particulate matter, and senescent erythrocytes from the blood.
• Pathway: Regulation of actin cytoskeleton - Homo sapiens (human);Integrin-mediated Cell Adhesion;Focal Adhesion;Overview of nanoparticle effects;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Integrin cell surface interactions;Extracellular matrix organization;Integrin;Beta2 integrin cell surface interactions (Consensus)

Intolerance Scores

• loftool: 0.604
• rvis_EVS: -0.52
• rvis_percentile_EVS: 20.97

Haploinsufficiency Scores

• pHI: 0.0644
• hipred: N
• hipred_score: 0.259

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itgad
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: immune response;integrin-mediated signaling pathway;extracellular matrix organization;heterotypic cell-cell adhesion
• Cellular component: plasma membrane;integrin complex;cell surface
• Molecular function: metal ion binding