ITGBL1

integrin subunit beta like 1, the group of Integrin beta subunits

Basic information

Region (hg38): 13:101452592-101720856

Links

ENSG00000198542 ∙ NCBI:9358 ∙ OMIM:604234 ∙ HGNC:6164 ∙ Uniprot:O95965 ∙ 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 ITGBL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGBL1 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					2	2
missense			29		2	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	4

Variants in ITGBL1

This is a list of pathogenic ClinVar variants found in the ITGBL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-101452874-C-T		not specified	Uncertain significance (Nov 09, 2022)
13-101453932-C-G		not specified	Uncertain significance (Dec 23, 2022)
13-101453941-G-C		not specified	Uncertain significance (May 09, 2024)
13-101453965-G-A		not specified	Uncertain significance (Jun 29, 2022)
13-101453975-A-G		not specified	Uncertain significance (Jan 09, 2024)
13-101453978-G-A		not specified	Uncertain significance (Feb 15, 2023)
13-101453980-C-T		not specified	Uncertain significance (Jan 18, 2023)
13-101453981-G-T		not specified	Uncertain significance (Feb 28, 2023)
13-101454087-G-C			Benign (Apr 04, 2018)
13-101567699-G-A			Benign (Jul 13, 2018)
13-101567770-A-G		not specified	Uncertain significance (Oct 27, 2023)
13-101567790-G-T		not specified	Uncertain significance (Feb 27, 2023)
13-101567827-A-T		not specified	Uncertain significance (Mar 31, 2023)
13-101579296-A-G		not specified	Uncertain significance (Dec 27, 2023)
13-101579297-G-T		not specified	Uncertain significance (May 23, 2023)
13-101579365-T-A		not specified	Uncertain significance (Feb 17, 2022)
13-101579386-G-A		not specified	Uncertain significance (Jun 16, 2024)
13-101583231-G-A		not specified	Uncertain significance (Nov 07, 2023)
13-101583273-G-A		not specified	Uncertain significance (Dec 13, 2022)
13-101583309-G-A		not specified	Uncertain significance (Aug 10, 2021)
13-101598189-A-G		not specified	Uncertain significance (May 01, 2022)
13-101598211-G-C		not specified	Uncertain significance (May 11, 2022)
13-101692615-A-G		not specified	Uncertain significance (Oct 26, 2021)
13-101692632-C-T		not specified	Uncertain significance (Oct 28, 2023)
13-101692666-G-A		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGBL1	protein_coding	protein_coding	ENST00000376180	11	270491

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.77e-9	0.848	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.582	247	274	0.901	0.0000147	3239
Missense in Polyphen		88	109.01	0.80723		1252
Synonymous	0.997	86	98.6	0.872	0.00000583	834
Loss of Function	1.67	18	27.5	0.655	0.00000128	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000855	0.000855
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000117	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000117	0.000109
South Asian	0.000196	0.000196
Other	0.000685	0.000652

dbNSFP

Source: dbNSFP

• Pathway: RUNX2 regulates genes involved in cell migration;Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.98

Haploinsufficiency Scores

• pHI: 0.177
• hipred: Y
• hipred_score: 0.540
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itgbl1

Zebrafish Information Network

• Gene name: itgbl1
• Affected structure: skeletal tissue
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: cell adhesion;cell-matrix adhesion;integrin-mediated signaling pathway;cell migration;cell adhesion mediated by integrin
• Cellular component: extracellular region;plasma membrane;focal adhesion;integrin complex;cell surface
• Molecular function: integrin binding