THAP3

THAP domain containing 3, the group of THAP domain containing

Basic information

Region (hg38): 1:6624867-6635586

Links

ENSG00000041988 ∙ NCBI:90326 ∙ OMIM:612532 ∙ HGNC:20855 ∙ Uniprot:Q8WTV1 ∙ 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 THAP3 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THAP3 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in THAP3

This is a list of pathogenic ClinVar variants found in the THAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-6625234-G-A		not specified	Uncertain significance (Jan 19, 2022)
1-6625240-C-T		not specified	Uncertain significance (Jun 29, 2022)
1-6625258-T-C		not specified	Uncertain significance (Aug 03, 2022)
1-6628632-C-T		not specified	Uncertain significance (Apr 07, 2022)
1-6628680-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-6632805-C-T		not specified	Likely benign (Feb 27, 2023)
1-6632812-C-T		not specified	Uncertain significance (Dec 06, 2021)
1-6632851-C-A		not specified	Uncertain significance (Jan 24, 2024)
1-6632947-A-G		not specified	Uncertain significance (Jul 25, 2023)
1-6632970-C-T		not specified	Uncertain significance (Jul 08, 2022)
1-6633010-G-T		not specified	Uncertain significance (Feb 06, 2024)
1-6633018-C-T		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THAP3	protein_coding	protein_coding	ENST00000054650	5	10721

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00728	0.785	125725	0	12	125737	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.204	135	142	0.952	0.00000908	1542
Missense in Polyphen		46	52.578	0.87489		566
Synonymous	-0.335	64	60.7	1.05	0.00000398	471
Loss of Function	0.959	4	6.67	0.599	2.83e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000450	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of a THAP1/THAP3-HCFC1-OGT complex that is required for the regulation of the transcriptional activity of RRM1. {ECO:0000269|PubMed:20200153}.

Recessive Scores

• pRec: 0.0983

Intolerance Scores

• loftool: 0.488
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.86

Haploinsufficiency Scores

• pHI: 0.0951
• hipred: N
• hipred_score: 0.153
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thap3

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding