GeneBe

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: 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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Corpus callosum, agenesis of, with impaired intellectual development, ocular coloboma and micrognathiaXLGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic14556245

ClinVar

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

  • not_specified (34 variants)
  • not_provided (11 variants)
  • IGBP1-related_disorder (4 variants)
  • Corpus_callosum_agenesis-intellectual_disability-coloboma-micrognathia_syndrome (4 variants)

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. These statistics are base on transcript: NM_000001551.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
3
clinvar
 6
missense
34
clinvar
3
clinvar
 37
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 34 6 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
IGBP1protein_codingprotein_codingENST00000342206 632876
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9830.017200000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.30901320.6810.000009972232
Missense in Polyphen825.6280.31216514
Synonymous-0.8725446.41.160.00000332620
Loss of Function3.26012.40.008.85e-7213

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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