TCL1B

TCL1 family AKT coactivator B

Basic information

Region (hg38): 14:95686426-95692628

Links

ENSG00000213231 ∙ NCBI:9623 ∙ OMIM:603769 ∙ HGNC:11649 ∙ Uniprot:O95988 ∙ 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 TCL1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCL1B 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						0
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in TCL1B

This is a list of pathogenic ClinVar variants found in the TCL1B region.

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

Position	Type	Phenotype	Significance	ClinVar
14-95686481-C-T		not specified	Uncertain significance (Apr 19, 2024)
14-95686489-C-T		not specified	Uncertain significance (Oct 26, 2021)
14-95686606-G-C		not specified	Uncertain significance (Jan 24, 2023)
14-95690818-C-T		not specified	Uncertain significance (Jul 21, 2021)
14-95690832-G-A		not specified	Likely benign (Dec 22, 2023)
14-95690863-G-A		not specified	Uncertain significance (Dec 17, 2023)
14-95691296-C-T		not specified	Uncertain significance (Jun 18, 2021)
14-95691298-T-C		not specified	Uncertain significance (Apr 06, 2022)
14-95691305-C-T		not specified	Uncertain significance (Jun 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCL1B	protein_coding	protein_coding	ENST00000340722	3	6227

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0101	0.838	125369	0	2	125371	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.212	76	81.4	0.934	0.00000506	819
Missense in Polyphen		24	23.765	1.0099		267
Synonymous	-2.29	51	34.0	1.50	0.00000223	259
Loss of Function	1.15	4	7.38	0.542	4.03e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances the phosphorylation and activation of AKT1 and AKT2. {ECO:0000269|PubMed:10983986}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway (Consensus)

Recessive Scores

• pRec: 0.0920

Intolerance Scores

• loftool: 0.535
• rvis_EVS: 0.81
• rvis_percentile_EVS: 87.82

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.213

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.697

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tcl1b5

Gene ontology

• Biological process: positive regulation of cell population proliferation;positive regulation of peptidyl-serine phosphorylation;positive regulation of protein serine/threonine kinase activity
• Cellular component: protein-containing complex
• Molecular function: protein kinase binding;protein serine/threonine kinase activator activity