TBL2

transducin beta like 2, the group of WD repeat domain containing

Basic information

Region (hg38): 7:73567536-73578791

Links

ENSG00000106638 ∙ NCBI:26608 ∙ OMIM:605842 ∙ HGNC:11586 ∙ Uniprot:Q9Y4P3 ∙ 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 TBL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBL2 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				4	2	6
missense			29	6	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	29	10	3

Variants in TBL2

This is a list of pathogenic ClinVar variants found in the TBL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-73570521-C-A		not specified	Uncertain significance (May 13, 2024)
7-73570570-C-G		not specified	Uncertain significance (Jan 24, 2024)
7-73570578-G-A		not specified	Uncertain significance (Mar 19, 2024)
7-73570583-C-T			Likely benign (Jan 05, 2018)
7-73570599-G-A		not specified	Uncertain significance (Jan 03, 2024)
7-73570619-T-C		not specified	Uncertain significance (Jun 09, 2022)
7-73570661-C-T		not specified	Uncertain significance (Jan 25, 2023)
7-73570667-G-A		not specified	Uncertain significance (Aug 17, 2021)
7-73570694-C-T		not specified	Uncertain significance (Nov 17, 2022)
7-73570742-C-T		not specified	Likely benign (Apr 17, 2023)
7-73570772-C-G		not specified	Uncertain significance (Oct 27, 2022)
7-73570829-G-C		not specified	Uncertain significance (May 13, 2024)
7-73570835-A-G		not specified	Uncertain significance (Jun 21, 2022)
7-73570844-C-T		not specified	Uncertain significance (May 20, 2024)
7-73570849-C-T			Likely benign (Jan 12, 2018)
7-73570853-G-A		not specified	Uncertain significance (May 15, 2024)
7-73570855-G-A			Benign/Likely benign (Apr 01, 2024)
7-73570908-T-G		not specified	Likely benign (Dec 08, 2023)
7-73570923-C-T		not specified	Uncertain significance (Mar 17, 2023)
7-73570951-A-T		not specified	Uncertain significance (Sep 16, 2021)
7-73570975-G-A			Likely benign (Dec 01, 2023)
7-73571192-C-T		not specified	Conflicting classifications of pathogenicity (Aug 05, 2023)
7-73571229-C-T		not specified	Uncertain significance (Dec 27, 2023)
7-73571260-C-A			Likely benign (Feb 07, 2018)
7-73571295-C-T		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBL2	protein_coding	protein_coding	ENST00000305632	7	9860

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000185	0.976	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.578	254	281	0.903	0.0000178	2915
Missense in Polyphen		63	77.016	0.81801		888
Synonymous	0.922	102	115	0.890	0.00000712	894
Loss of Function	2.02	9	18.3	0.492	0.00000103	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000253	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=TBL2 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of TBL2 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease.

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.565
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.61

Haploinsufficiency Scores

• pHI: 0.248
• hipred: N
• hipred_score: 0.237
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.849

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tbl2

Gene ontology

• Biological process: endoplasmic reticulum unfolded protein response;cellular response to glucose starvation;cellular response to hypoxia
• Cellular component: endoplasmic reticulum;integral component of endoplasmic reticulum membrane
• Molecular function: RNA binding;protein kinase binding;translation initiation factor binding;phosphoprotein binding