THAP11

THAP domain containing 11, the group of THAP domain containing

Basic information

Region (hg38): 16:67842320-67844195

Links

ENSG00000168286 ∙ NCBI:57215 ∙ OMIM:609119 ∙ HGNC:23194 ∙ Uniprot:Q96EK4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• methylmalonic aciduria and homocystinuria (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Allelic with Methylmalonic aciduria, cblC type-like (AR)	AD	Biochemical	A described individual was affected with severe neurologic sequelae and while treatment (eg, with protein restriction,betaine, folic acid, hydroxocobalamin injection, and pyridoxine) was not effective, it would be logical to implement such management for this type of biochemical condition	Biochemical; Neurologic	28449119; 37148549; 38757579

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the THAP11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THAP11 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			3	17	6	26
missense		1	31			32
nonsense						0
start loss						0
frameshift						0
inframe indel			20	42	5	67
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	1	54	59	12

Variants in THAP11

This is a list of pathogenic ClinVar variants found in the THAP11 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67842450-G-A			Benign (May 15, 2021)
16-67842563-C-G		THAP11-related disorder	Benign (Oct 16, 2024)
16-67842572-C-T		not specified • THAP11-related disorder	Benign (Jan 14, 2025)
16-67842592-A-G		not specified	Uncertain significance (Aug 02, 2023)
16-67842635-A-C			Uncertain significance (Jan 04, 2024)
16-67842674-G-A			Likely benign (Apr 20, 2022)
16-67842689-C-T			Likely benign (Nov 15, 2021)
16-67842773-G-A			Likely benign (Jul 24, 2024)
16-67842779-C-G			Likely benign (Mar 20, 2023)
16-67842791-C-T			Likely benign (Mar 16, 2024)
16-67842794-C-G		Methylmalonic acidemia with homocystinuria, type cblX • Disorders of Intracellular Cobalamin Metabolism • Methylmalonic aciduria and homocystinuria, cb1L type	Likely pathogenic (Dec 07, 2016)
16-67842794-C-T			Benign (Jan 13, 2025)
16-67842811-A-G			Uncertain significance (Aug 31, 2021)
16-67842852-G-T		not specified	Uncertain significance (Jun 03, 2022)
16-67842862-GGCAGCA-G			Benign (Jul 08, 2024)
16-67842862-GGCAGCAGCA-G			Likely benign (Aug 04, 2023)
16-67842862-GGCAGCAGCAGCAACAGCA-G			Likely benign (Nov 19, 2024)
16-67842862-G-GGCA			Uncertain significance (Jul 03, 2024)
16-67842862-G-GGCAGCAGCAGCAACAGCA			Likely benign (Dec 02, 2024)
16-67842862-G-GGCAGCAGCAGCAACA			Likely benign (May 25, 2022)
16-67842863-GCAGCAGCAGCAA-G			Likely benign (Apr 25, 2024)
16-67842863-G-GCAGCAGCAGCAA			Uncertain significance (Jun 18, 2024)
16-67842865-A-G		not specified	Uncertain significance (Mar 02, 2024)
16-67842866-GCAGCAGCAA-G			Likely benign (Sep 16, 2024)
16-67842866-GCAGCAGCAACAGCAGCAGCAGCAGCAA-G			Uncertain significance (Oct 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THAP11	protein_coding	protein_coding	ENST00000303596	1	1885

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.826	0.173	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	98	179	0.547	0.00000822	1998
Missense in Polyphen		3	25.158	0.11924		287
Synonymous	-3.08	110	75.9	1.45	0.00000371	656
Loss of Function	2.66	1	10.1	0.0986	4.46e-7	104

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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that plays a central role for embryogenesis and the pluripotency of embryonic stem (ES) cells. Sequence-specific DNA-binding factor that represses gene expression in pluripotent ES cells by directly binding to key genetic loci and recruiting epigenetic modifiers (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.358
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.492
• hipred: N
• hipred_score: 0.425
• ghis: 0.444

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.613

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thap11
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: thap11
• Affected structure: ceratobranchial cartilage
• Phenotype tag: abnormal
• Phenotype quality: immature

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm;cytoplasm;intercellular bridge
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding