ITGB1BP1
integrin subunit beta 1 binding protein 1
Basic information
Region (hg38): 2:9403475-9423528
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGB1BP1 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in ITGB1BP1
This is a list of pathogenic ClinVar variants found in the ITGB1BP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-9406847-G-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 2-9406860-A-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 2-9406860-A-T | not specified | Uncertain significance (Apr 20, 2023) | ||
| 2-9406872-T-C | not specified | Uncertain significance (May 27, 2022) | ||
| 2-9407531-G-A | not specified | Uncertain significance (Oct 25, 2024) | ||
| 2-9407598-C-A | not specified | Uncertain significance (Apr 18, 2023) | ||
| 2-9408148-T-G | not specified | Uncertain significance (Apr 22, 2024) | ||
| 2-9408151-A-G | not specified | Uncertain significance (Sep 27, 2021) | ||
| 2-9408174-T-G | not specified | Uncertain significance (Nov 24, 2024) | ||
| 2-9412366-C-T | not specified | Uncertain significance (Oct 27, 2022) | ||
| 2-9418691-G-A | not specified | Uncertain significance (Nov 07, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ITGB1BP1 | protein_coding | protein_coding | ENST00000360635 | 6 | 20073 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000970 | 0.813 | 125716 | 0 | 32 | 125748 | 0.000127 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.712 | 91 | 112 | 0.811 | 0.00000598 | 1300 |
| Missense in Polyphen | 39 | 42.303 | 0.92192 | 525 | ||
| Synonymous | -0.141 | 45 | 43.8 | 1.03 | 0.00000269 | 373 |
| Loss of Function | 1.22 | 8 | 12.7 | 0.631 | 7.98e-7 | 136 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000217 | 0.000213 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.000274 | 0.000272 |
| Finnish | 0.000185 | 0.000185 |
| European (Non-Finnish) | 0.000132 | 0.000132 |
| Middle Eastern | 0.000274 | 0.000272 |
| South Asian | 0.0000655 | 0.0000653 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Key regulator of the integrin-mediated cell-matrix interaction signaling by binding to the ITGB1 cytoplasmic tail and preventing the activation of integrin alpha-5/beta-1 (heterodimer of ITGA5 and ITGB1) by talin or FERMT1. Plays a role in cell proliferation, differentiation, spreading, adhesion and migration in the context of mineralization and bone development and angiogenesis. Stimulates cellular proliferation in a fibronectin- dependent manner. Involved in the regulation of beta-1 integrin- containing focal adhesion (FA) site dynamics by controlling its assembly rate during cell adhesion; inhibits beta-1 integrin clustering within FA by directly competing with talin TLN1, and hence stimulates osteoblast spreading and migration in a fibronectin-and/or collagen-dependent manner. Acts as a guanine nucleotide dissociation inhibitor (GDI) by regulating Rho family GTPases during integrin-mediated cell matrix adhesion; reduces the level of active GTP-bound form of both CDC42 and RAC1 GTPases upon cell adhesion to fibronectin. Stimulates the release of active CDC42 from the membranes to maintain it in an inactive cytoplasmic pool. Participates in the translocation of the Rho-associated protein kinase ROCK1 to membrane ruffles at cell leading edges of the cell membrane, leading to an increase of myoblast cell migration on laminin. Plays a role in bone mineralization at a late stage of osteoblast differentiation; modulates the dynamic formation of focal adhesions into fibrillar adhesions, which are adhesive structures responsible for fibronectin deposition and fibrillogenesis. Plays a role in blood vessel development; acts as a negative regulator of angiogenesis by attenuating endothelial cell proliferation and migration, lumen formation and sprouting angiogenesis by promoting AKT phosphorylation and inhibiting ERK1/2 phosphorylation through activation of the Notch signaling pathway. Promotes transcriptional activity of the MYC promoter. {ECO:0000269|PubMed:11741838, ECO:0000269|PubMed:11807099, ECO:0000269|PubMed:11919189, ECO:0000269|PubMed:12473654, ECO:0000269|PubMed:15703214, ECO:0000269|PubMed:17916086, ECO:0000269|PubMed:20616313, ECO:0000269|PubMed:21768292, ECO:0000269|Ref.19}.;
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.361
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.486
- hipred
- N
- hipred_score
- 0.401
- ghis
- 0.619
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Itgb1bp1
- Phenotype
- craniofacial phenotype; growth/size/body region phenotype; skeleton phenotype; vision/eye phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- blood vessel endothelial cell proliferation involved in sprouting angiogenesis;negative regulation of protein kinase activity;negative regulation of cell adhesion involved in substrate-bound cell migration;cell-matrix adhesion;Notch signaling pathway;integrin-mediated signaling pathway;positive regulation of cell population proliferation;negative regulation of cell population proliferation;positive regulation of endothelial cell migration;negative regulation of fibroblast migration;protein transport;cell migration;cell differentiation;biomineral tissue development;negative regulation of protein binding;activation of protein kinase B activity;integrin activation;regulation of cell adhesion mediated by integrin;tube formation;intracellular signal transduction;cellular response to vascular endothelial growth factor stimulus;regulation of GTPase activity;receptor clustering;cellular response to fibroblast growth factor stimulus;positive regulation of Notch signaling pathway;positive regulation of transcription by RNA polymerase II;regulation of blood vessel size;myoblast migration;positive regulation of stress fiber assembly;positive regulation of cell division;positive regulation of focal adhesion assembly;negative regulation of focal adhesion assembly;positive regulation of protein kinase B signaling;negative regulation of ERK1 and ERK2 cascade;negative regulation of cell migration involved in sprouting angiogenesis;positive regulation of protein targeting to membrane;negative regulation of protein targeting to membrane;negative regulation of substrate adhesion-dependent cell spreading;regulation of integrin-mediated signaling pathway
- Cellular component
- ruffle;nucleus;nucleoplasm;cytoplasm;microtubule organizing center;cytosol;cytoskeleton;plasma membrane;focal adhesion;membrane;nuclear body;lamellipodium;perinuclear region of cytoplasm;cell periphery
- Molecular function
- GDP-dissociation inhibitor activity;integrin binding;protein binding;protein transporter activity;protein kinase binding;protein-containing complex binding