CSF2RB

colony stimulating factor 2 receptor subunit beta, the group of CD molecules|Fibronectin type III domain containing

Basic information

Region (hg38): 22:36913628-36940439

Previous symbols: [ "IL3RB" ]

Links

ENSG00000100368 ∙ NCBI:1439 ∙ OMIM:138981 ∙ HGNC:2436 ∙ Uniprot:P32927 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• surfactant metabolism dysfunction, pulmonary, 5 (Moderate), mode of inheritance: AR
• hereditary pulmonary alveolar proteinosis (Supportive), mode of inheritance: AR
• surfactant metabolism dysfunction, pulmonary, 5 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Surfactant metabolism dysfunction, pulmonary, 5	AR	Pulmonary	The condition typically manifests with childhood-onset respiratory insufficiency (though adult-onset disease has also been reported) due to pulmonary alveolar proteinosis, and whole-lung lavage may be beneficial; It has been reported that diagnosis has important therapeutic implications, as BMT/HSCT can be effective	Pulmonary	9410898; 21075760

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSF2RB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSF2RB 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			6	153	11	170
missense			319	8	6	333
nonsense		1	6			7
start loss			1			1
frameshift			10			10
inframe indel			2			2
splice donor/acceptor (+/-2bp)			1	1		2
splice region			8	12		20
non coding				64	38	102
Total	0	1	345	226	55

Variants in CSF2RB

This is a list of pathogenic ClinVar variants found in the CSF2RB region.

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

Position	Type	Phenotype	Significance	ClinVar
22-36921806-T-C			Benign (Nov 10, 2018)
22-36921872-C-T			Benign (Jun 10, 2019)
22-36921928-A-G			Benign (Nov 10, 2018)
22-36921972-G-T			Benign (Nov 10, 2018)
22-36921991-C-T			Benign (Nov 27, 2018)
22-36922079-T-G			Likely benign (May 26, 2019)
22-36922133-C-T			Likely benign (Jun 10, 2019)
22-36922208-A-T			Uncertain significance (Jun 09, 2022)
22-36922215-T-A			Uncertain significance (Nov 10, 2022)
22-36922224-G-T			Uncertain significance (Oct 14, 2023)
22-36922235-A-G			Uncertain significance (Nov 03, 2023)
22-36922243-G-A			Likely benign (Oct 04, 2022)
22-36922263-G-A			Uncertain significance (Jan 05, 2023)
22-36922264-C-T			Likely benign (Oct 07, 2023)
22-36922267-C-A		CSF2RB-related disorder	Benign/Likely benign (Mar 01, 2024)
22-36922275-G-C			Uncertain significance (Sep 05, 2023)
22-36922276-G-A			Benign (Jan 29, 2024)
22-36922287-A-G			Uncertain significance (Mar 10, 2023)
22-36922292-C-T			Likely benign (Jun 10, 2022)
22-36922293-G-A			Likely benign (Mar 02, 2023)
22-36922297-C-T			Likely benign (Aug 06, 2022)
22-36922384-C-T			Benign (Nov 10, 2018)
22-36922404-G-A			Benign (Nov 10, 2018)
22-36922437-G-A			Benign (Mar 24, 2019)
22-36922473-T-C			Benign (Nov 10, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSF2RB	protein_coding	protein_coding	ENST00000403662	13	26822

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.176	0.824	125268	2	478	125748	0.00191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.129	518	526	0.984	0.0000325	5759
Missense in Polyphen		77	96.251	0.79999		1260
Synonymous	-1.81	258	224	1.15	0.0000148	1901
Loss of Function	4.00	8	32.7	0.245	0.00000161	342

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000904	0.000904
Ashkenazi Jewish	0.0246	0.0247
East Asian	0.000163	0.000163
Finnish	0.00106	0.00106
European (Non-Finnish)	0.00142	0.00142
Middle Eastern	0.000163	0.000163
South Asian	0.0000980	0.0000980
Other	0.00228	0.00228

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High affinity receptor for interleukin-3, interleukin-5 and granulocyte-macrophage colony-stimulating factor.
• Disease: DISEASE: Pulmonary surfactant metabolism dysfunction 5 (SMDP5) [MIM:614370]: A rare lung disorder due to impaired surfactant homeostasis. It is characterized by alveolar filling with floccular material that stains positive using the periodic acid- Schiff method and is derived from surfactant phospholipids and protein components. Excessive lipoproteins accumulation in the alveoli results in severe respiratory distress. {ECO:0000269|PubMed:21075760}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Apoptosis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);IL-5 Signaling Pathway;IL-3 Signaling Pathway;Signaling by GPCR;IL-3 signaling;Signal Transduction;Signaling by Interleukins;regulation of bad phosphorylation;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Surfactant metabolism;Metabolism of proteins;il 3 signaling pathway;Immune System;Interleukin receptor SHC signaling;Interleukin-2 family signaling;IL5-mediated signaling events;KitReceptor;IL-5 signaling;JAK STAT MolecularVariation 2;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;JAK STAT pathway and regulation;IL3;IL5;G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;GMCSF-mediated signaling events;IL3-mediated signaling events;Interleukin-3, 5 and GM-CSF signaling (Consensus)

Recessive Scores

• pRec: 0.249

Intolerance Scores

• loftool: 0.0832
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.32

Haploinsufficiency Scores

• pHI: 0.311
• hipred: N
• hipred_score: 0.429
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.698

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csf2rb2
• Phenotype: normal phenotype; hematopoietic system phenotype; respiratory system phenotype; immune system phenotype

Gene ontology

• Biological process: MAPK cascade;signal transduction;respiratory gaseous exchange;peptidyl-tyrosine phosphorylation;cytokine-mediated signaling pathway;response to lipopolysaccharide;cellular response to interleukin-3;interleukin-5-mediated signaling pathway;interleukin-3-mediated signaling pathway;cellular protein metabolic process
• Cellular component: plasma membrane;integral component of plasma membrane;granulocyte macrophage colony-stimulating factor receptor complex
• Molecular function: protein tyrosine kinase activity;interleukin-3 receptor activity;interleukin-5 receptor activity;Ras guanyl-nucleotide exchange factor activity;protein binding;signaling receptor activity