THRAP3

thyroid hormone receptor associated protein 3, the group of WTAP complex|Spliceosomal A complex

Basic information

Region (hg38): 1:36224432-36305357

Links

ENSG00000054118 ∙ NCBI:9967 ∙ OMIM:603809 ∙ HGNC:22964 ∙ Uniprot:Q9Y2W1 ∙ 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 THRAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THRAP3 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			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1		1
Total	0	0	36	2	0

Variants in THRAP3

This is a list of pathogenic ClinVar variants found in the THRAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-36282606-C-T		not specified	Uncertain significance (Nov 09, 2022)
1-36282607-G-A		not specified	Uncertain significance (May 05, 2023)
1-36282667-G-A		not specified	Uncertain significance (Mar 20, 2024)
1-36282679-G-A		not specified	Uncertain significance (Nov 29, 2023)
1-36286514-C-T		not specified	Uncertain significance (Jun 13, 2023)
1-36286541-A-G		not specified	Uncertain significance (Dec 15, 2022)
1-36286565-A-G		not specified	Uncertain significance (Oct 05, 2023)
1-36286579-G-T		not specified	Uncertain significance (Nov 07, 2022)
1-36286688-G-A		not specified	Uncertain significance (Apr 11, 2023)
1-36286697-G-A		not specified	Uncertain significance (May 23, 2023)
1-36286738-G-C		not specified	Uncertain significance (Apr 22, 2024)
1-36286810-G-A		not specified	Uncertain significance (May 26, 2022)
1-36286933-C-T		not specified	Uncertain significance (Jun 02, 2023)
1-36286963-C-G		not specified	Uncertain significance (Aug 22, 2023)
1-36286963-C-T		not specified	Uncertain significance (Nov 09, 2022)
1-36286985-A-G		not specified	Uncertain significance (Jul 27, 2022)
1-36287026-C-T		not specified	Uncertain significance (Nov 09, 2021)
1-36287063-C-A		not specified	Uncertain significance (Jun 13, 2024)
1-36287102-C-T		not specified	Uncertain significance (May 02, 2024)
1-36287113-T-G		not specified	Likely benign (Apr 28, 2023)
1-36289060-G-A		not specified	Likely benign (Nov 13, 2023)
1-36289065-T-C		not specified	Uncertain significance (Apr 09, 2024)
1-36289121-G-A		not specified	Uncertain significance (Oct 05, 2022)
1-36289239-A-G		not specified	Uncertain significance (Jan 04, 2022)
1-36289265-G-A		not specified	Uncertain significance (May 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THRAP3	protein_coding	protein_coding	ENST00000354618	10	80942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000201	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	416	560	0.743	0.0000347	6194
Missense in Polyphen		197	236.85	0.83175		2986
Synonymous	-0.0994	194	192	1.01	0.00000971	1886
Loss of Function	5.89	4	48.1	0.0832	0.00000346	527

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing. Remains associated with spliced mRNA after splicing which probably involves interactions with the exon junction complex (EJC). Can trigger mRNA decay which seems to be independent of nonsense-mediated decay involving premature stop codons (PTC) recognition. May be involved in nuclear mRNA decay. Involved in regulation of signal-induced alternative splicing. During splicing of PTPRC/CD45 is proposed to sequester phosphorylated SFPQ from PTPRC/CD45 pre-mRNA in resting T-cells. Involved in cyclin-D1/CCND1 mRNA stability probably by acting as component of the SNARP complex which associates with both the 3'end of the CCND1 gene and its mRNA. Involved in response to DNA damage. Is excluced from DNA damage sites in a manner that parallels transcription inhibition; the function may involve the SNARP complex. Initially thought to play a role in transcriptional coactivation through its association with the TRAP complex; however, it is not regarded as a stable Mediator complex subunit. Cooperatively with HELZ2, enhances the transcriptional activation mediated by PPARG, maybe through the stabilization of the PPARG binding to DNA in presence of ligand. May play a role in the terminal stage of adipocyte differentiation. Plays a role in the positive regulation of the circadian clock. Acts as a coactivator of the CLOCK-ARNTL/BMAL1 heterodimer and promotes its transcriptional activator activity and binding to circadian target genes (PubMed:24043798). {ECO:0000269|PubMed:20123736, ECO:0000269|PubMed:20932480, ECO:0000269|PubMed:22424773, ECO:0000269|PubMed:23525231, ECO:0000269|PubMed:24043798}.
• Pathway: Interactome of polycomb repressive complex 2 (PRC2);Developmental Biology;Transcriptional regulation of white adipocyte differentiation (Consensus)

Recessive Scores

• pRec: 0.255

Intolerance Scores

• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.4

Haploinsufficiency Scores

• pHI: 0.245
• hipred: Y
• hipred_score: 0.825
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thrap3

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;nuclear-transcribed mRNA catabolic process;transcription initiation from RNA polymerase II promoter;mRNA processing;circadian rhythm;RNA splicing;intracellular steroid hormone receptor signaling pathway;androgen receptor signaling pathway;positive regulation of circadian rhythm;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of mRNA splicing, via spliceosome;mRNA stabilization
• Cellular component: nucleus;nucleoplasm;mediator complex;nuclear speck;exon-exon junction complex;extracellular exosome
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;transcription coregulator activity;transcription coactivator activity;RNA binding;protein binding;ATP binding;nuclear receptor transcription coactivator activity;signaling receptor activity;vitamin D receptor binding;thyroid hormone receptor binding;phosphoprotein binding