THAP2

THAP domain containing 2, the group of THAP domain containing

Basic information

Region (hg38): 12:71664301-71680644

Links

ENSG00000173451 ∙ NCBI:83591 ∙ OMIM:612531 ∙ HGNC:20854 ∙ Uniprot:Q9H0W7 ∙ 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 THAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THAP2 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			7
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	0	0

Variants in THAP2

This is a list of pathogenic ClinVar variants found in the THAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-71664547-C-G		not specified	Uncertain significance (Feb 23, 2023)
12-71674223-G-A		not specified	Uncertain significance (Sep 17, 2021)
12-71674372-G-T		not specified	Uncertain significance (Jan 30, 2024)
12-71674387-A-G		not specified	Uncertain significance (Sep 26, 2022)
12-71676743-C-A		not specified	Uncertain significance (Mar 15, 2024)
12-71676834-T-A		not specified	Uncertain significance (May 17, 2023)
12-71677053-A-C		not specified	Uncertain significance (Jul 26, 2022)
12-71677079-C-G		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THAP2	protein_coding	protein_coding	ENST00000308086	3	17631

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-7	0.128	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.219	111	118	0.943	0.00000570	1504
Missense in Polyphen		60	62.466	0.96052		784
Synonymous	0.910	33	40.4	0.818	0.00000185	425
Loss of Function	-0.236	10	9.23	1.08	6.16e-7	111

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000325	0.000325
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000888	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.483
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• pHI: 0.0481
• hipred: N
• hipred_score: 0.195
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thap2

Gene ontology

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