TCL1A

TCL1 family AKT coactivator A

Basic information

Region (hg38): 14:95709946-95714196

Links

ENSG00000100721

∙ NCBI:8115 ∙ OMIM:186960 ∙ HGNC:11648 ∙ Uniprot:P56279 ∙ 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 TCL1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCL1A 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			5 clinvar		1 clinvar	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	1

Variants in TCL1A

This is a list of pathogenic ClinVar variants found in the TCL1A region.

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

Position	Phenotype	Significance	ClinVar
14-95712239-C-T	not specified	Uncertain significance (Sep 27, 2021)	2343828
14-95712336-G-A	not specified	Uncertain significance (Jun 02, 2023)	2540125
14-95713979-T-G	not specified	Uncertain significance (Jan 24, 2024)	3175301
14-95713997-A-T	not specified	Uncertain significance (Jan 24, 2024)	3175300
14-95714032-G-A	not specified	Uncertain significance (Oct 12, 2022)	2318191
14-95714036-C-T		Benign (Apr 26, 2018)	789821

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TCL1A	protein_coding	protein_coding	ENST00000402399	3	4230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.74e-10	0.0183	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.319	70	77.9	0.898	0.00000530	713
Missense in Polyphen		14	25.236	0.55477		259
Synonymous	0.355	32	34.7	0.923	0.00000257	224
Loss of Function	-1.21	12	8.26	1.45	5.37e-7	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000982	0.0000879
Middle Eastern	0.0000545	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, AKT2 and AKT3. Promotes nuclear translocation of AKT1. Enhances cell proliferation, stabilizes mitochondrial membrane potential and promotes cell survival. {ECO:0000269|PubMed:10716693, ECO:0000269|PubMed:10983986, ECO:0000269|PubMed:11707444, ECO:0000269|PubMed:11839817}.;
Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;BCR (Consensus)

Recessive Scores

pRec: 0.168

Intolerance Scores

loftool: 0.661
rvis_EVS: 0.5
rvis_percentile_EVS: 79.89

Haploinsufficiency Scores

pHI: 0.0454
hipred: N
hipred_score: 0.153
ghis: 0.408

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.793

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tcl1
Phenotype: reproductive system phenotype;

Gene ontology

Biological process: multicellular organism development;positive regulation of cell population proliferation;positive regulation of mitochondrial membrane potential;positive regulation of protein oligomerization;positive regulation of peptidyl-serine phosphorylation;negative regulation of apoptotic process;protein homotrimerization;cellular response to tumor necrosis factor;positive regulation of protein serine/threonine kinase activity
Cellular component: nucleus;endoplasmic reticulum;protein-containing complex
Molecular function: protein binding;protein kinase binding;identical protein binding;protein serine/threonine kinase activator activity