THAP12

THAP domain containing 12, the group of THAP domain containing

Basic information

Region (hg38): 11:76349897-76381132

Previous symbols: [ "PRKRIR" ]

Links

ENSG00000137492 ∙ NCBI:5612 ∙ OMIM:607374 ∙ HGNC:9440 ∙ Uniprot:O43422 ∙ 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 THAP12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THAP12 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in THAP12

This is a list of pathogenic ClinVar variants found in the THAP12 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-76350960-T-G		not specified	Uncertain significance (Jul 06, 2021)
11-76351044-C-T			Likely benign (Nov 01, 2022)
11-76351421-T-C		not specified	Uncertain significance (Nov 16, 2021)
11-76352213-T-C		not specified	Uncertain significance (Jul 20, 2021)
11-76352354-C-T		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THAP12	protein_coding	protein_coding	ENST00000260045	5	31016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.968	0.0317	125724	0	16	125740	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.34	251	379	0.662	0.0000188	5030
Missense in Polyphen		15	52.685	0.28471		823
Synonymous	0.366	137	143	0.961	0.00000744	1422
Loss of Function	4.24	4	28.3	0.141	0.00000174	358

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000855	0.0000791
Middle Eastern	0.000167	0.000163
South Asian	0.0000669	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Upstream regulator of interferon-induced serine/threonine protein kinase R (PKR). May block the PKR- inhibitory function of DNAJC3, resulting in restoration of kinase activity and suppression of cell growth.

Recessive Scores

• pRec: 0.201

Intolerance Scores

• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.617
• hipred: Y
• hipred_score: 0.728
• ghis: 0.576

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Thap12

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;signal transduction;negative regulation of cell population proliferation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding;protein dimerization activity