ZBTB11

zinc finger and BTB domain containing 11, the group of Zinc fingers C2H2-type|BTB domain containing

Basic information

Region (hg38): 3:101648889-101677135

Links

ENSG00000066422 ∙ NCBI:27107 ∙ OMIM:618181 ∙ HGNC:16740 ∙ Uniprot:O95625 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder, autosomal recessive 69 (Strong), mode of inheritance: AR
• intellectual developmental disorder, autosomal recessive 69 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with progressive movement abnormalities, cognitive decline, and brain abnormalities	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	29893856

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZBTB11 gene.

• Intellectual developmental disorder, autosomal recessive 69 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB11 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				7		7
missense			70	5		75
nonsense	1		3			4
start loss						0
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	2	0	74	12	0

Variants in ZBTB11

This is a list of pathogenic ClinVar variants found in the ZBTB11 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-101651152-CTTCA-C		ZBTB11-related disorder	Likely benign (Jun 21, 2019)
3-101651191-A-G		not specified	Uncertain significance (Oct 04, 2022)
3-101651308-G-A		not specified	Uncertain significance (Jul 25, 2023)
3-101651351-T-C		not specified	Uncertain significance (Nov 13, 2023)
3-101651383-T-C			Uncertain significance (Jan 04, 2024)
3-101651414-T-C		not specified	Uncertain significance (Jun 17, 2022)
3-101651527-G-C		not specified	Uncertain significance (Aug 02, 2021)
3-101651549-G-A		Intellectual developmental disorder, autosomal recessive 69	Pathogenic (Oct 30, 2024)
3-101651568-G-A		ZBTB11-related disorder	Likely benign (Apr 01, 2019)
3-101651594-G-A		Intellectual developmental disorder, autosomal recessive 69	Pathogenic (Oct 30, 2024)
3-101651605-T-C		not specified	Uncertain significance (Jan 31, 2025)
3-101651620-C-T		Intellectual developmental disorder, autosomal recessive 69	Pathogenic (Oct 30, 2024)
3-101651654-C-T		not specified	Uncertain significance (Oct 17, 2023)
3-101651660-T-C		Intellectual developmental disorder, autosomal recessive 69	Pathogenic (Oct 30, 2024)
3-101651673-T-G			Likely benign (Aug 01, 2024)
3-101651685-TAA-T		ZBTB11-related disorder	Likely benign (Oct 24, 2019)
3-101652500-A-C		Intellectual developmental disorder, autosomal recessive 69	Pathogenic (Oct 30, 2024)
3-101652522-T-C			Uncertain significance (Feb 14, 2022)
3-101652553-A-AT			Uncertain significance (Mar 26, 2022)
3-101652568-G-A		not specified	Uncertain significance (Jan 12, 2024)
3-101652785-A-C			Likely benign (Mar 01, 2022)
3-101652802-G-A			Uncertain significance (Dec 29, 2022)
3-101652832-T-G			Uncertain significance (Dec 29, 2022)
3-101652849-T-A		not specified	Uncertain significance (Sep 02, 2024)
3-101652903-C-A		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB11	protein_coding	protein_coding	ENST00000312938	11	28607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000320	1.00	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	424	560	0.757	0.0000282	6858
Missense in Polyphen		149	255.03	0.58425		3058
Synonymous	-1.66	232	202	1.15	0.0000100	2003
Loss of Function	4.20	19	51.5	0.369	0.00000303	622

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000151	0.000151
Ashkenazi Jewish	0.000203	0.000198
East Asian	0.000219	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000209	0.000202
Middle Eastern	0.000219	0.000217
South Asian	0.000165	0.000163
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.641
• rvis_EVS: -1.3
• rvis_percentile_EVS: 4.92

Haploinsufficiency Scores

• pHI: 0.350
• hipred: Y
• hipred_score: 0.575
• ghis: 0.655

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb11

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;biological_process
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA binding;metal ion binding