ZBTB40

zinc finger and BTB domain containing 40, the group of BTB domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 1:22428838-22531157

Links

ENSG00000184677 ∙ NCBI:9923 ∙ OMIM:612106 ∙ HGNC:29045 ∙ Uniprot:Q9NUA8 ∙ 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 ZBTB40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB40 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	3	6
missense			54	6	2	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1		1
Total	0	0	54	10	5

Variants in ZBTB40

This is a list of pathogenic ClinVar variants found in the ZBTB40 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-22490042-A-G		not specified	Uncertain significance (Feb 17, 2024)
1-22490142-T-C		not specified	Uncertain significance (Jan 23, 2023)
1-22490181-T-G		not specified	Uncertain significance (Jun 06, 2023)
1-22490194-A-G			Benign (Feb 26, 2018)
1-22490340-C-T		not specified	Likely benign (Jan 31, 2024)
1-22490378-C-G		not specified	Uncertain significance (Oct 10, 2023)
1-22490400-C-A		not specified	Uncertain significance (Feb 06, 2023)
1-22490597-C-G		not specified	Uncertain significance (Nov 03, 2023)
1-22490610-C-T		not specified	Uncertain significance (Mar 22, 2023)
1-22491503-G-A		ZBTB40-related disorder	Benign (Feb 26, 2018)
1-22501498-G-A		not specified	Likely benign (Jul 05, 2023)
1-22501505-G-A		not specified	Uncertain significance (May 16, 2023)
1-22501509-C-T		ZBTB40-related disorder	Likely benign (Oct 23, 2019)
1-22501529-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-22501551-T-C			Benign (Aug 24, 2018)
1-22501576-G-A		not specified	Uncertain significance (Jun 10, 2024)
1-22501585-G-C		not specified	Uncertain significance (Mar 21, 2023)
1-22501585-G-T		not specified	Uncertain significance (Feb 22, 2023)
1-22501670-C-T		not specified	Uncertain significance (Oct 27, 2022)
1-22502317-A-G		not specified	Uncertain significance (May 10, 2024)
1-22502326-C-A		not specified	Uncertain significance (Oct 12, 2021)
1-22502377-T-C		not specified	Uncertain significance (Aug 10, 2023)
1-22502418-T-C		not specified	Uncertain significance (Aug 23, 2021)
1-22502436-A-C		not specified	Uncertain significance (Oct 04, 2022)
1-22506110-G-A		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB40	protein_coding	protein_coding	ENST00000404138	17	79307

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.05e-10	1.00	125637	1	110	125748	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	564	642	0.878	0.0000352	8146
Missense in Polyphen		14	22.935	0.61043		259
Synonymous	0.300	255	261	0.976	0.0000154	2395
Loss of Function	3.31	25	50.4	0.496	0.00000246	678

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000755	0.000692
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000164	0.000163
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.000705	0.000686
Middle Eastern	0.000164	0.000163
South Asian	0.000327	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.524
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.74

Haploinsufficiency Scores

• pHI: 0.324
• hipred: N
• hipred_score: 0.414
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb40

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cellular response to DNA damage stimulus;bone mineralization
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA binding;metal ion binding