ITGB1BP2

integrin subunit beta 1 binding protein 2

Basic information

Region (hg38): X:71301750-71305371

Links

ENSG00000147166 ∙ NCBI:26548 ∙ OMIM:300332 ∙ HGNC:6154 ∙ Uniprot:Q9UKP3 ∙ 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 ITGB1BP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGB1BP2 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			16	2	2	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	17	3	2

Variants in ITGB1BP2

This is a list of pathogenic ClinVar variants found in the ITGB1BP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-71301822-C-T		not specified	Uncertain significance (Mar 19, 2024)
X-71301843-C-T			Benign (Dec 31, 2019)
X-71302148-C-T		not specified	Uncertain significance (May 24, 2023)
X-71302273-T-C			Benign (Jul 06, 2018)
X-71302305-T-G			Benign (Aug 11, 2018)
X-71302543-C-T		not specified	Uncertain significance (Feb 05, 2024)
X-71303288-C-T		not specified	Uncertain significance (Jul 09, 2024)
X-71303478-C-T			Likely benign (Dec 31, 2019)
X-71303479-G-A		not specified	Likely benign (Jul 02, 2024)
X-71303646-G-C		not specified	Uncertain significance (Feb 20, 2025)
X-71303648-G-T		not specified	Uncertain significance (Nov 12, 2021)
X-71303685-G-A		not specified	Uncertain significance (Jan 29, 2024)
X-71303817-A-G		not specified	Uncertain significance (Jan 09, 2024)
X-71303859-C-T		not specified	Uncertain significance (Apr 25, 2022)
X-71304193-G-C		not specified	Uncertain significance (Feb 13, 2024)
X-71304197-C-T		not specified	Uncertain significance (Jan 24, 2024)
X-71304253-C-G		not specified	Uncertain significance (Dec 27, 2022)
X-71304259-C-A		not specified	Uncertain significance (Apr 26, 2023)
X-71304268-G-A		not specified	Uncertain significance (Jan 28, 2025)
X-71304270-G-A			Likely benign (May 08, 2018)
X-71304546-A-G		not specified	Uncertain significance (Mar 20, 2023)
X-71304567-G-A		not specified	Uncertain significance (Nov 30, 2022)
X-71304575-G-A		not specified	Uncertain significance (Dec 26, 2023)
X-71304600-G-T		not specified	Uncertain significance (Jan 31, 2025)
X-71304972-A-G		not specified	Uncertain significance (Nov 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGB1BP2	protein_coding	protein_coding	ENST00000373829	11	3638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.60e-8	0.292	125685	17	41	125743	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.779	107	132	0.809	0.00000983	2276
Missense in Polyphen		38	41.954	0.90575		732
Synonymous	1.17	37	47.2	0.784	0.00000339	647
Loss of Function	0.580	13	15.5	0.841	0.00000120	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00105	0.000923
Ashkenazi Jewish	0.00	0.00
East Asian	0.000289	0.000217
Finnish	0.000728	0.000323
European (Non-Finnish)	0.000362	0.000185
Middle Eastern	0.000289	0.000217
South Asian	0.000315	0.000196
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role during maturation and/or organization of muscles cells.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.568
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.244
• ghis: 0.478

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: Itgb1bp2
• 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: signal transduction;muscle organ development
• Cellular component: Z disc
• Molecular function: integrin binding;calcium ion binding;protein binding;zinc ion binding;SH3 domain binding