TBPL1

TATA-box binding protein like 1

Basic information

Region (hg38): 6:133952169-133990432

Links

ENSG00000028839

∙ NCBI:9519 ∙ OMIM:605521 ∙ HGNC:11589 ∙ Uniprot:P62380 ∙ 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 TBPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBPL1 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in TBPL1

This is a list of pathogenic ClinVar variants found in the TBPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-133984459-G-C		not specified	Uncertain significance (May 04, 2022)	2402921
6-133984621-C-G		not specified	Uncertain significance (Nov 29, 2023)	3174881

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBPL1	protein_coding	protein_coding	ENST00000237264	6	38263

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.379	0.611	125470	0	2	125472	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.50	30	101	0.298	0.00000533	1209
Missense in Polyphen		8	34.599	0.23122		397
Synonymous	1.74	19	31.4	0.606	0.00000154	354
Loss of Function	2.18	2	9.09	0.220	3.81e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Part of a specialized transcription system that mediates the transcription of most ribosomal proteins through the 5'-TCT-3' motif which is a core promoter element at these genes. Seems to also mediate the transcription of NF1. Does not bind the TATA box. {ECO:0000269|PubMed:10082669, ECO:0000269|PubMed:10220372, ECO:0000269|PubMed:15767669, ECO:0000269|PubMed:24958592}.;
Pathway: Huntington,s disease - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Basal transcription factors - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.240

Intolerance Scores

loftool
rvis_EVS: 0.32
rvis_percentile_EVS: 72.94

Haploinsufficiency Scores

pHI: 0.715
hipred: Y
hipred_score: 0.825
ghis: 0.459

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tbpl1
Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype;

Gene ontology

Biological process: acrosome assembly;dTTP biosynthetic process;transcription by RNA polymerase II;spermatid nucleus differentiation;positive regulation of transcription by RNA polymerase II;RNA polymerase III preinitiation complex assembly
Cellular component: transcription factor TFIIIB complex;transcription factor complex;transcription factor TFIID complex;transcription factor TFIIA complex;cytoplasm
Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase III regulatory region DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;transcription factor binding