TBPL2

TATA-box binding protein like 2

Basic information

Region (hg38): 14:55414210-55456726

Links

ENSG00000182521

∙ NCBI:387332 ∙ OMIM:608964 ∙ HGNC:19841 ∙ Uniprot:Q6SJ96 ∙ 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 TBPL2 gene.

not_specified (38 variants)
not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TBPL2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000199047.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			38 clinvar			38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	0	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TBPL2	protein_coding	protein_coding	ENST00000247219	7	43186

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.49e-10	0.110	125358	2	388	125748	0.00155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.324	218	205	1.06	0.0000107	2431
Missense in Polyphen		43	56.411	0.76227		710
Synonymous	-0.285	84	80.7	1.04	0.00000453	758
Loss of Function	0.335	16	17.5	0.914	9.73e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0135	0.0135
European (Non-Finnish)	0.000478	0.000457
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00310	0.00310

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcription factor required in complex with TAF3 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process (By similarity). {ECO:0000250|UniProtKB:Q6SJ95}.;
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: 0.113

Intolerance Scores

loftool: 0.817
rvis_EVS: 0.11
rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

pHI: 0.649
hipred: N
hipred_score: 0.161
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.548

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tbpl2
Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype;

Zebrafish Information Network

Gene name: tbpl2
Affected structure: trunk
Phenotype tag: abnormal
Phenotype quality: curvature

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;multicellular organism development;negative regulation of transcription, DNA-templated;RNA polymerase III preinitiation complex assembly
Cellular component: transcription factor TFIIIB complex;nucleus;transcription factor complex;transcription factor TFIID 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 factor activity;transcription factor binding