THAP10

THAP domain containing 10, the group of THAP domain containing

Basic information

Region (hg38): 15:70881342-70892433

Links

ENSG00000129028 ∙ NCBI:56906 ∙ OMIM:612538 ∙ HGNC:23193 ∙ Uniprot:Q9P2Z0 ∙ 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 THAP10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THAP10 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in THAP10

This is a list of pathogenic ClinVar variants found in the THAP10 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-70882482-G-A		not specified	Uncertain significance (Feb 15, 2023)
15-70882564-G-C		not specified	Uncertain significance (Jan 17, 2023)
15-70882594-T-C		not specified	Uncertain significance (Dec 07, 2021)
15-70882769-C-T		not specified	Uncertain significance (May 02, 2024)
15-70882827-A-C		not specified	Uncertain significance (Jan 09, 2024)
15-70882904-G-A		not specified	Uncertain significance (Sep 16, 2021)
15-70891870-C-A		not specified	Uncertain significance (Jun 11, 2021)
15-70891879-G-A		not specified	Uncertain significance (Jun 28, 2023)
15-70891911-G-C		not specified	Uncertain significance (Jan 08, 2024)
15-70891959-T-A		not specified	Uncertain significance (Feb 16, 2023)
15-70891987-C-A		not specified	Uncertain significance (Nov 13, 2023)
15-70892001-C-T		not specified	Uncertain significance (Aug 17, 2022)
15-70892071-C-T		not specified	Uncertain significance (Mar 11, 2022)
15-70892124-C-A		not specified	Uncertain significance (Apr 04, 2023)
15-70892125-G-A		not specified	Uncertain significance (Dec 21, 2023)
15-70892181-A-G		not specified	Uncertain significance (Jun 16, 2024)
15-70892188-C-T		not specified	Uncertain significance (Dec 01, 2022)
15-70892191-C-T		not specified	Uncertain significance (Mar 23, 2023)
15-70892194-G-A		not specified	Uncertain significance (May 05, 2023)
15-70892217-G-C		not specified	Uncertain significance (May 29, 2024)
15-70892248-G-A		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THAP10	protein_coding	protein_coding	ENST00000249861	3	11444

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0458	0.862	110997	0	1	110998	0.00000450

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.480	132	148	0.889	0.00000707	1650
Missense in Polyphen		24	35.146	0.68286		403
Synonymous	-0.584	64	58.3	1.10	0.00000281	541
Loss of Function	1.38	3	6.93	0.433	2.99e-7	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
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	0.0000394	0.0000394
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0675

Intolerance Scores

• loftool: 0.475
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.0805
• hipred: N
• hipred_score: 0.153
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.840

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
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding