THAP9

THAP domain containing 9, the group of THAP domain containing

Basic information

Region (hg38): 4:82900684-82919969

Links

ENSG00000168152 ∙ NCBI:79725 ∙ OMIM:612537 ∙ HGNC:23192 ∙ Uniprot:Q9H5L6 ∙ 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 THAP9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THAP9 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				1		1
missense			41	1		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	2	0

Variants in THAP9

This is a list of pathogenic ClinVar variants found in the THAP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-82904764-A-G		not specified	Uncertain significance (Jun 28, 2022)
4-82906432-A-G		not specified	Uncertain significance (Sep 26, 2022)
4-82906463-T-C		not specified	Uncertain significance (Jan 04, 2024)
4-82906508-T-C		not specified	Uncertain significance (Jan 04, 2024)
4-82906511-C-A		not specified	Uncertain significance (Jun 29, 2023)
4-82906512-C-G			Likely benign (Apr 01, 2023)
4-82906513-G-C		not specified	Uncertain significance (Aug 02, 2023)
4-82906519-A-G		not specified	Uncertain significance (May 30, 2024)
4-82906561-G-A		not specified	Uncertain significance (Apr 24, 2024)
4-82906565-C-T		not specified	Uncertain significance (Dec 22, 2023)
4-82907800-T-C		not specified	Uncertain significance (Aug 16, 2022)
4-82907802-T-C		not specified	Uncertain significance (Jan 17, 2023)
4-82907832-G-A		not specified	Likely benign (May 03, 2023)
4-82907868-T-C		not specified	Uncertain significance (Feb 13, 2024)
4-82907898-A-C		not specified	Uncertain significance (Apr 25, 2023)
4-82916975-T-C		not specified	Uncertain significance (Jun 10, 2024)
4-82916982-G-A		not specified	Uncertain significance (Jul 05, 2022)
4-82917014-G-C		not specified	Uncertain significance (Aug 09, 2021)
4-82917018-A-G		not specified	Uncertain significance (Aug 22, 2023)
4-82917027-A-G		not specified	Uncertain significance (Jul 06, 2022)
4-82917030-T-G		not specified	Uncertain significance (Jun 18, 2021)
4-82917035-C-G		not specified	Uncertain significance (Dec 21, 2023)
4-82917180-T-C		not specified	Uncertain significance (Mar 15, 2024)
4-82917186-T-C		not specified	Uncertain significance (Jun 21, 2021)
4-82917201-T-G		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THAP9	protein_coding	protein_coding	ENST00000302236	5	19286

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.99e-13	0.699	125619	0	129	125748	0.000513

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	370	457	0.810	0.0000221	5945
Missense in Polyphen		67	118.51	0.56537		1549
Synonymous	0.925	153	168	0.909	0.00000819	1699
Loss of Function	1.65	24	34.5	0.697	0.00000199	434

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00135	0.00133
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00174	0.00174
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000294	0.000281
Middle Eastern	0.00174	0.00174
South Asian	0.000987	0.000980
Other	0.000521	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Active transposase that specifically recognizes the bipartite 5'-TXXGGGX(A/T)-3' consensus motif and mediates transposition. {ECO:0000269|PubMed:20010837, ECO:0000269|PubMed:23349291}.

Recessive Scores

• pRec: 0.0934

Intolerance Scores

• loftool: 0.275
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.53

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.225
• ghis: 0.462

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0618

Gene Damage Prediction

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

Gene ontology

• Biological process: DNA recombination;transposition, DNA-mediated;regulation of transcription by RNA polymerase II;DNA integration
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;transposase activity;transferase activity;sequence-specific DNA binding;metal ion binding