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.

not_provided (119 variants)
not_specified (27 variants)
THAP11-related_disorder (14 variants)
Disorders_of_Intracellular_Cobalamin_Metabolism (1 variants)
Methylmalonic_aciduria_and_homocystinuria,_cb1L_type (1 variants)
Methylmalonic_acidemia_with_homocystinuria,_type_cblX (1 variants)

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. These statistics are base on transcript: NM_000020457.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	18 clinvar	5 clinvar	27
missense		1 clinvar	43 clinvar			44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	47	18	5

Loading clinvar variants...

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