THAP5

THAP domain containing 5, the group of THAP domain containing

Basic information

Region (hg38): 7:108554542-108569750

Links

ENSG00000177683 ∙ NCBI:168451 ∙ OMIM:612534 ∙ HGNC:23188 ∙ Uniprot:Q7Z6K1 ∙ 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 THAP5 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THAP5 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	0

Variants in THAP5

This is a list of pathogenic ClinVar variants found in the THAP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-108564418-C-G		not specified	Uncertain significance (Jul 20, 2022)
7-108564422-T-A		not specified	Uncertain significance (Nov 08, 2021)
7-108564510-G-A		not specified	Uncertain significance (Dec 05, 2022)
7-108564580-T-G		not specified	Uncertain significance (Dec 09, 2023)
7-108564627-G-A		not specified	Uncertain significance (May 26, 2022)
7-108564663-C-G		not specified	Uncertain significance (Oct 03, 2022)
7-108564663-C-T		not specified	Likely benign (Aug 02, 2021)
7-108564670-A-G		not specified	Uncertain significance (Dec 14, 2022)
7-108564681-G-A		not specified	Uncertain significance (Jun 10, 2022)
7-108564769-T-C		not specified	Uncertain significance (Feb 15, 2023)
7-108564987-A-T		not specified	Uncertain significance (Apr 12, 2022)
7-108564988-C-T		not specified	Uncertain significance (Jun 05, 2023)
7-108565015-C-T		not specified	Uncertain significance (Mar 29, 2022)
7-108565846-A-C		not specified	Uncertain significance (Feb 06, 2023)
7-108566012-G-T		not specified	Uncertain significance (Oct 02, 2023)
7-108569523-C-T		not specified	Uncertain significance (Dec 11, 2023)
7-108569530-G-C		not specified	Uncertain significance (May 31, 2022)
7-108569544-C-T		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THAP5	protein_coding	protein_coding	ENST00000415914	3	15208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000862	0.777	125648	0	50	125698	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.130	183	188	0.973	0.00000839	2606
Missense in Polyphen		49	53.434	0.91702		736
Synonymous	1.07	55	66.1	0.832	0.00000309	728
Loss of Function	1.22	10	15.1	0.661	7.74e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000292	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000264	0.000264
Middle Eastern	0.000381	0.000381
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has sequence-specific DNA-binding activity and can function as transcriptional repressor (in vitro) (PubMed:21110952). May be a regulator of cell cycle: THAP5 overexpression in human cell lines causes cell cycle arrest at G2/M phase (PubMed:19502560). {ECO:0000269|PubMed:21110952, ECO:0000305|PubMed:19502560}.

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• loftool: 0.381
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.0966
• hipred: N
• hipred_score: 0.146
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Gene ontology

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