CTNNBL1

catenin beta like 1, the group of NineTeen complex|Spliceosomal C complex|Armadillo like helical domain containing

Basic information

Region (hg38): 20:37693954-37872129

Previous symbols: [ "C20orf33" ]

Links

ENSG00000132792 ∙ NCBI:56259 ∙ OMIM:611537 ∙ HGNC:15879 ∙ Uniprot:Q8WYA6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 99 with hypogammaglobulinemia and autoimmune cytopenias (Limited), mode of inheritance: Unknown
• common variable immunodeficiency (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 99 with hypogammaglobulinemia and autoimmune cytopenias	AR	Allergy/Immunology/Infectious	The condition can include early-onset, frequent sinopulmonary infections, and awareness may enable prophylactic measures and early and agressive treatment of infections	Allergy/Immunology/Infectious; Hematologic	32484799

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTNNBL1 gene.

• Inborn genetic diseases (13 variants)
• not provided (5 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTNNBL1 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		3
missense			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	13	5	2

Variants in CTNNBL1

This is a list of pathogenic ClinVar variants found in the CTNNBL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-37732901-C-T			Uncertain significance (Nov 01, 2022)
20-37732970-A-G		not specified	Uncertain significance (Dec 19, 2022)
20-37737456-C-T		not specified	Uncertain significance (Oct 26, 2022)
20-37746497-A-G		not specified	Uncertain significance (Mar 04, 2024)
20-37746512-T-C		not specified	Uncertain significance (Oct 11, 2023)
20-37746669-T-C		not specified	Benign (Jan 24, 2024)
20-37768027-C-G			Likely benign (Apr 20, 2018)
20-37777412-A-G		not specified	Uncertain significance (Dec 21, 2023)
20-37802913-G-A		not specified	Uncertain significance (Sep 30, 2021)
20-37802979-A-G		not specified	Uncertain significance (Apr 08, 2022)
20-37803011-G-T		not specified	Uncertain significance (Dec 13, 2022)
20-37803039-G-A		not specified	Uncertain significance (Dec 08, 2023)
20-37840135-G-A		not specified	Uncertain significance (May 24, 2023)
20-37840168-TG-T		not specified	Uncertain significance (Feb 29, 2024)
20-37842378-G-A		not specified	Uncertain significance (Dec 06, 2022)
20-37842380-A-G			Likely benign (Dec 01, 2022)
20-37842392-G-A			Likely benign (Dec 01, 2022)
20-37859902-A-G		Immunodeficiency 99 with hypogammaglobulinemia and autoimmune cytopenias	Pathogenic (Apr 27, 2022)
20-37859930-A-G		not specified	Likely benign (Nov 12, 2021)
20-37859951-A-G		not specified	Uncertain significance (Jul 19, 2023)
20-37860035-A-T		not specified	Uncertain significance (Oct 22, 2021)
20-37860275-C-T		not specified	Uncertain significance (Apr 18, 2023)
20-37860326-G-A		not specified	Uncertain significance (Jan 08, 2024)
20-37860333-A-G		not specified	Uncertain significance (Sep 14, 2021)
20-37871911-C-A		not specified	Benign (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTNNBL1	protein_coding	protein_coding	ENST00000361383	16	178124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00971	0.990	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.18	231	345	0.670	0.0000209	3759
Missense in Polyphen		64	108.55	0.5896		1192
Synonymous	0.981	116	130	0.891	0.00000774	1037
Loss of Function	3.74	10	33.3	0.300	0.00000194	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000795	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing. Participates in AID/AICDA-mediated Ig class switching recombination (CSR). May induce apoptosis.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.215

Intolerance Scores

• loftool: 0.589
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.203
• hipred: Y
• hipred_score: 0.750
• ghis: 0.608

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.843

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctnnbl1
• Phenotype: immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: mRNA splicing, via spliceosome;apoptotic process;somatic diversification of immunoglobulins;positive regulation of apoptotic process
• Cellular component: Prp19 complex;nucleus;nucleoplasm;spliceosomal complex;cytoplasm;membrane
• Molecular function: protein binding;enzyme binding