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.

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.

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					2	2
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	2		3
Total	0	0	18	2	2

Variants in TBPL2

This is a list of pathogenic ClinVar variants found in the TBPL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-55414444-G-A		not specified	Uncertain significance (May 18, 2023)
14-55424161-G-A		not specified	Uncertain significance (Jan 16, 2024)
14-55424215-A-G		not specified	Uncertain significance (May 23, 2024)
14-55424216-T-C		not specified	Uncertain significance (Nov 29, 2021)
14-55424252-A-G		not specified	Uncertain significance (May 17, 2023)
14-55428815-C-T			Benign (Apr 04, 2018)
14-55428858-C-G		not specified	Uncertain significance (Oct 10, 2023)
14-55428899-G-A			Benign (Feb 01, 2023)
14-55428910-C-G		not specified	Uncertain significance (Dec 06, 2023)
14-55428933-A-G		not specified	Uncertain significance (Sep 21, 2023)
14-55428937-G-A		not specified	Uncertain significance (Dec 19, 2022)
14-55433690-T-C		not specified	Uncertain significance (May 04, 2023)
14-55433691-C-T		not specified	Uncertain significance (Jan 06, 2023)
14-55435900-A-C		not specified	Uncertain significance (Nov 02, 2023)
14-55436728-G-C		not specified	Uncertain significance (Oct 10, 2023)
14-55436754-C-T		not specified	Uncertain significance (Sep 17, 2021)
14-55436786-T-G		not specified	Uncertain significance (Nov 12, 2021)
14-55436931-C-T		not specified	Uncertain significance (Feb 27, 2023)
14-55436939-G-A		not specified	Uncertain significance (Jul 14, 2021)
14-55440418-T-C		not specified	Uncertain significance (Jul 20, 2022)
14-55440442-T-C		not specified	Uncertain significance (Jun 29, 2023)
14-55440469-G-C		not specified	Uncertain significance (Apr 05, 2023)
14-55440487-G-A		not specified	Likely benign (Jan 16, 2024)
14-55440499-G-C		not specified	Likely benign (Dec 20, 2023)

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

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