ITGB1BP2

protein-coding

integrin subunit beta 1 binding protein 2

Gene summary

This gene encodes a protein with two cysteine and histidine-rich (CHORD) domains, PXXP motifs, YXXI/P motifs, putative SH2 and SH3 domain binding motifs, and an acidic region at the C-terminus that can bind calcium. Two hybrid analysis showed that this protein interacts with the cytoplasmic domain of the beta 1 integrin subunit and is thought to act as a chaperone protein. Studies in the mouse ortholog of this gene indicate that absence of this gene in mouse results in failed cardiac hypertrophy in response to mechanical stress. Alternative splicing results in multiple transcript variants encoding different isoforms, including an isoform that lacks several domains, including one of the CHORD domains. [provided by RefSeq, May 2017]

MANE transcript

NM_012278.4

Inheritance

—

ClinVar variants

U:56B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chrX:71,301,750-71,305,371

External References & Databases

Ensembl (ENSG00000147166)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ITGB1BP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012278.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			49 clinvar	3 clinvar	2 clinvar	54
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	56	4	2	62

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012278.4	RefSeq	NP_036410.1	11	MANE Select
ENST00000373829.8	Ensembl	ENSP00000362935.3	11	MANE Select
NM_001303277.3	RefSeq	NP_001290206.1	7	Standard
ENST00000538820.1	Ensembl	ENSP00000440289.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

signal transduction
muscle organ development

Molecular Function

integrin binding
calcium ion binding
protein binding
zinc ion binding
SH3 domain binding

Cellular Component

Z disc

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373829
Coding exons: 11
Length: 3638
Individuals with no LoFs: 125685
Homozygous LoFs: 17
Heterozygous LoFs: 41
Defined: 125743
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.779	107	132	0.809	0.00000983	2276
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00055	rare
Latino/Admixed American	0.00037	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00029	0.00022	rare
Finnish	0.00073	0.00032	rare
European (Non-Finnish)	0.00036	0.00018	rare
South Asian	0.00031	0.00020	rare
Other	0.00022	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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