IGBP1

immunoglobulin binding protein 1, the group of Protein phosphatase 2 modulatory subunits

Basic information

Region (hg38): X:70133447-70166324

Previous symbols: [ "IBP1" ]

Links

ENSG00000089289 ∙ NCBI:3476 ∙ OMIM:300139 ∙ HGNC:5461 ∙ Uniprot:P78318 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome (Limited), mode of inheritance: XLR
• corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome (Limited), mode of inheritance: AD
• corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome (Supportive), mode of inheritance: XL
• corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome (Limited), mode of inheritance: XL
• corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome (Limited), mode of inheritance: Unknown
• corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome (Disputed Evidence), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Corpus callosum, agenesis of, with impaired intellectual development, ocular coloboma and micrognathia	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	14556245

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IGBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGBP1 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				3	2	5
missense			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2			2
non coding				1	5	6
Total	0	0	18	7	7

Variants in IGBP1

This is a list of pathogenic ClinVar variants found in the IGBP1 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-70133891-TAT-AA		Corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome	Pathogenic (Nov 15, 2003)
X-70133893-T-A			Likely benign (Dec 01, 2023)
X-70133952-C-G			Uncertain significance (Aug 30, 2017)
X-70133962-C-T			Benign (Apr 06, 2018)
X-70133974-G-T		not specified	Conflicting classifications of pathogenicity (Mar 01, 2022)
X-70133984-C-G		Corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome	Uncertain significance (May 05, 2020)
X-70134042-C-A		not specified	Uncertain significance (Apr 07, 2023)
X-70134046-C-T			Benign (Dec 31, 2019)
X-70134600-C-T		Corpus callosum agenesis-intellectual disability-coloboma-micrognathia syndrome	Uncertain significance (Sep 18, 2020)
X-70134637-T-C			Likely benign (Nov 01, 2017)
X-70134651-G-A		not specified	Benign/Likely benign (Dec 31, 2019)
X-70134657-A-G		not specified	Uncertain significance (Feb 09, 2023)
X-70134688-C-G		not specified	Uncertain significance (Apr 08, 2022)
X-70134714-C-T		IGBP1-related disorder	Uncertain significance (Jan 09, 2023)
X-70134744-A-T		not specified	Uncertain significance (Apr 26, 2024)
X-70146686-T-C		IGBP1-related disorder • not specified	Uncertain significance (Apr 18, 2023)
X-70146704-A-G		not specified	Uncertain significance (Oct 27, 2023)
X-70146711-G-C		not specified	Uncertain significance (May 02, 2024)
X-70146713-G-A		not specified	Uncertain significance (Nov 25, 2024)
X-70146728-A-G		not specified	Uncertain significance (Sep 02, 2024)
X-70146747-G-A		IGBP1-related disorder	Benign (Dec 31, 2019)
X-70146758-T-C		not specified	Benign/Likely benign (Dec 31, 2019)
X-70148782-C-T		not specified	Uncertain significance (Feb 28, 2023)
X-70148797-C-T		not specified	Uncertain significance (Jul 13, 2021)
X-70148800-G-C		IGBP1-related disorder	Uncertain significance (Sep 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGBP1	protein_coding	protein_coding	ENST00000342206	6	32876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0172	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	90	132	0.681	0.00000997	2232
Missense in Polyphen		8	25.628	0.31216		514
Synonymous	-0.872	54	46.4	1.16	0.00000332	620
Loss of Function	3.26	0	12.4	0.00	8.85e-7	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associated to surface IgM-receptor; may be involved in signal transduction. Involved in regulation of the catalytic activity of the phosphatases PP2A, PP4 and PP6 by protecting their partially folded catalytic subunits from degradative polyubiquitination until they associate with regulatory subunits. {ECO:0000269|PubMed:19818709, ECO:0000269|PubMed:23591866}.
• Disease: DISEASE: Mental retardation, X-linked, syndromic, 28 (MRXS28) [MIM:300472]: A mental retardation syndrome characterized by agenesis of the corpus callosum, coloboma of the iris and optic nerve, severe retrognathia, and intellectual deficit. Mental retardation is defined by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:14556245}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.136
• hipred: Y
• hipred_score: 0.783
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.310

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igbp1
• Phenotype: hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;signal transduction;negative regulation of stress-activated MAPK cascade;response to tumor necrosis factor;B cell activation;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;regulation of phosphoprotein phosphatase activity;regulation of microtubule-based movement;response to interleukin-1
• Cellular component: cytoplasm;cytosol
• Molecular function: protein binding;protein phosphatase regulator activity;protein phosphatase 2A binding