IBSP

integrin binding sialoprotein, the group of SIBLING family

Basic information

Region (hg38): 4:87799553-87812435

Links

ENSG00000029559 ∙ NCBI:3381 ∙ OMIM:147563 ∙ HGNC:5341 ∙ Uniprot:P21815 ∙ 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 IBSP gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IBSP 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			6	1		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	6	1	0

Variants in IBSP

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

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

Position	Type	Phenotype	Significance	ClinVar
4-87802690-C-T			Likely benign (May 24, 2018)
4-87806127-T-G		not specified	Uncertain significance (Mar 14, 2024)
4-87810640-C-T		not specified	Uncertain significance (Jun 12, 2023)
4-87811443-G-A		not specified	Uncertain significance (Feb 21, 2024)
4-87811451-C-A		not specified	Uncertain significance (Nov 10, 2022)
4-87811452-G-A		not specified	Uncertain significance (Feb 27, 2024)
4-87811536-G-A		not specified	Uncertain significance (Jun 22, 2023)
4-87811546-A-T		not specified	Uncertain significance (Dec 20, 2023)
4-87811608-G-C		not specified	Uncertain significance (Jul 20, 2021)
4-87811779-T-C		not specified	Uncertain significance (Feb 21, 2024)
4-87811824-T-C		not specified	Uncertain significance (Feb 07, 2023)
4-87811902-C-A		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IBSP	protein_coding	protein_coding	ENST00000226284	6	12342

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-11	0.0527	125650	0	92	125742	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.464	156	173	0.901	0.00000937	2072
Missense in Polyphen		59	63.805	0.92469		809
Synonymous	0.684	60	67.1	0.894	0.00000440	553
Loss of Function	0.103	17	17.5	0.973	0.00000106	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00165	0.00164
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000275	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000308	0.000299
Middle Eastern	0.000275	0.000272
South Asian	0.000305	0.000261
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds tightly to hydroxyapatite. Appears to form an integral part of the mineralized matrix. Probably important to cell-matrix interaction. Promotes Arg-Gly-Asp-dependent cell attachment.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Interleukin-11 Signaling Pathway;Human Complement System;Focal Adhesion;Osteoblast Signaling;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;regulators of bone mineralization;Integrin cell surface interactions;Extracellular matrix organization;Beta3 integrin cell surface interactions;ECM proteoglycans (Consensus)

Recessive Scores

• pRec: 0.356

Intolerance Scores

• loftool: 0.877
• rvis_EVS: 1.35
• rvis_percentile_EVS: 94.35

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0774

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ibsp
• Phenotype: skeleton phenotype; immune system phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype; hematopoietic system phenotype; craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: osteoblast differentiation;cell adhesion;extracellular matrix organization;bone mineralization;positive regulation of cell adhesion;cellular response to growth factor stimulus
• Cellular component: extracellular region;extracellular space;membrane;vesicle
• Molecular function: molecular_function;integrin binding