THAP4

THAP domain containing 4, the group of THAP domain containing

Basic information

Region (hg38): 2:241584405-241637158

Links

ENSG00000176946 ∙ NCBI:51078 ∙ OMIM:612533 ∙ HGNC:23187 ∙ Uniprot:Q8WY91 ∙ 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 THAP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THAP4 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			38	3		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	3	0

Variants in THAP4

This is a list of pathogenic ClinVar variants found in the THAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-241584610-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-241584643-T-C		not specified	Uncertain significance (Aug 30, 2021)
2-241584661-G-A		not specified	Uncertain significance (May 31, 2023)
2-241584679-G-A		not specified	Uncertain significance (Nov 18, 2023)
2-241601997-C-T		not specified	Uncertain significance (Nov 13, 2023)
2-241602982-C-A		not specified	Uncertain significance (Jan 16, 2024)
2-241603020-C-T		not specified	Uncertain significance (Apr 06, 2024)
2-241603050-T-G		not specified	Uncertain significance (Jan 22, 2024)
2-241606353-A-G		not specified	Uncertain significance (Apr 06, 2024)
2-241606395-C-G		not specified	Uncertain significance (May 25, 2022)
2-241606396-C-T		not specified	Uncertain significance (May 01, 2022)
2-241606456-G-A		not specified	Uncertain significance (Feb 03, 2022)
2-241606471-G-A		not specified	Uncertain significance (Jun 02, 2023)
2-241633007-C-T		not specified	Uncertain significance (Aug 20, 2023)
2-241633043-C-T		not specified	Uncertain significance (Feb 12, 2024)
2-241633096-T-G		not specified	Uncertain significance (Dec 21, 2023)
2-241633108-A-G		not specified	Uncertain significance (Mar 15, 2024)
2-241633175-T-C		not specified	Uncertain significance (May 14, 2024)
2-241633195-C-T		not specified	Uncertain significance (Sep 06, 2022)
2-241633286-C-T		not specified	Uncertain significance (Sep 20, 2023)
2-241633435-G-A		not specified	Uncertain significance (Feb 05, 2024)
2-241633505-T-C		not specified	Uncertain significance (Jun 24, 2022)
2-241633525-G-A		not specified	Uncertain significance (Mar 24, 2023)
2-241633531-C-T		not specified	Uncertain significance (Jul 25, 2023)
2-241633538-C-T		not specified	Uncertain significance (Apr 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THAP4	protein_coding	protein_coding	ENST00000407315	6	53045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.276	0.723	125738	0	6	125744	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	261	363	0.719	0.0000226	3741
Missense in Polyphen		91	171.46	0.53075		1786
Synonymous	-0.101	164	162	1.01	0.0000117	1187
Loss of Function	3.24	5	21.0	0.238	0.00000115	239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.0521
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.45

Haploinsufficiency Scores

• pHI: 0.448
• hipred: Y
• hipred_score: 0.532
• ghis: 0.509

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.493

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thap4

Gene ontology

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