ITGB3BP

integrin subunit beta 3 binding protein, the group of Constitutive centromere associated network

Basic information

Region (hg38): 1:63440769-63593721

Links

ENSG00000142856 ∙ NCBI:23421 ∙ OMIM:605494 ∙ HGNC:6157 ∙ Uniprot:Q13352 ∙ 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 ITGB3BP gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGB3BP 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						0
missense			4			4
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	4	0	0

Variants in ITGB3BP

This is a list of pathogenic ClinVar variants found in the ITGB3BP region.

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

Position	Type	Phenotype	Significance	ClinVar
1-63446850-C-G		not specified	Uncertain significance (Jan 23, 2023)
1-63453963-T-C		not specified	Uncertain significance (Aug 04, 2023)
1-63453969-T-C		not specified	Uncertain significance (Feb 21, 2024)
1-63454426-A-C		not specified	Uncertain significance (Feb 27, 2024)
1-63454895-T-C		not specified	Uncertain significance (Jul 12, 2022)
1-63454964-T-C		not specified	Uncertain significance (Apr 25, 2022)
1-63454968-T-C		not specified	Likely benign (Aug 15, 2023)
1-63525594-G-A		not specified	Uncertain significance (Jul 15, 2021)
1-63525597-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-63525624-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-63525747-C-A		not specified	Uncertain significance (Jun 03, 2022)
1-63531841-A-G		not specified	Uncertain significance (Nov 21, 2022)
1-63532716-T-G		not specified	Uncertain significance (Jun 29, 2023)
1-63532754-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-63533523-A-G			Benign (Feb 25, 2018)
1-63534124-A-G		not specified	Uncertain significance (Jan 19, 2024)
1-63534182-G-A		not specified	Likely benign (Mar 05, 2024)
1-63545939-AG-A		Postaxial polydactyly	Uncertain significance (-)
1-63545947-T-G		not specified	Uncertain significance (Dec 28, 2022)
1-63551817-G-A		not specified	Uncertain significance (Nov 29, 2023)
1-63557137-A-C		not specified	Uncertain significance (Mar 22, 2023)
1-63561706-CAG-C		Postaxial polydactyly	Uncertain significance (-)
1-63561723-A-G		not specified	Uncertain significance (Nov 09, 2023)
1-63561775-C-T		not specified	Uncertain significance (Apr 11, 2023)
1-63561783-C-G		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGB3BP	protein_coding	protein_coding	ENST00000371092	9	152952

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.96e-7	0.324	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.494	78	91.3	0.854	0.00000422	1409
Missense in Polyphen		12	17.918	0.66973		303
Synonymous	-0.0445	30	29.7	1.01	0.00000138	363
Loss of Function	0.483	11	12.9	0.855	6.02e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000886	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000362	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription coregulator that can have both coactivator and corepressor functions. Isoform 1, but not other isoforms, is involved in the coactivation of nuclear receptors for retinoid X (RXRs) and thyroid hormone (TRs) in a ligand-dependent fashion. In contrast, it does not coactivate nuclear receptors for retinoic acid, vitamin D, progesterone receptor, nor glucocorticoid. Acts as a coactivator for estrogen receptor alpha. Acts as a transcriptional corepressor via its interaction with the NFKB1 NF- kappa-B subunit, possibly by interfering with the transactivation domain of NFKB1. Induces apoptosis in breast cancer cells, but not in other cancer cells, via a caspase-2 mediated pathway that involves mitochondrial membrane permeabilization but does not require other caspases. May also act as an inhibitor of cyclin A- associated kinase. Also acts a component of the CENPA-CAD (nucleosome distal) complex, a complex recruited to centromeres which is involved in assembly of kinetochore proteins, mitotic progression and chromosome segregation. May be involved in incorporation of newly synthesized CENPA into centromeres via its interaction with the CENPA-NAC complex. {ECO:0000269|PubMed:11713274, ECO:0000269|PubMed:12244126, ECO:0000269|PubMed:15082778, ECO:0000269|PubMed:15254226, ECO:0000269|PubMed:16622420}.
• Pathway: Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;Nucleosome assembly;RHO GTPase Effectors;Signaling by Rho GTPases;Chromosome Maintenance;NRIF signals cell death from the nucleus;Deposition of new CENPA-containing nucleosomes at the centromere;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;Cell death signalling via NRAGE, NRIF and NADE (Consensus)

Recessive Scores

• pRec: 0.0856

Intolerance Scores

• loftool: 0.753
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.0902
• hipred: N
• hipred_score: 0.412
• ghis: 0.658

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.229

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itgb3bp

Gene ontology

• Biological process: regulation of transcription, DNA-templated;apoptotic process;cell cycle;cell adhesion;signal transduction;CENP-A containing nucleosome assembly;positive regulation of apoptotic process;cell division
• Cellular component: condensed chromosome kinetochore;nucleus;nucleoplasm;cytoplasm;cytosol;membrane
• Molecular function: protein binding;protein C-terminus binding