ZBTB42

zinc finger and BTB domain containing 42, the group of BTB domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 14:104800595-104804712

Links

ENSG00000179627 ∙ NCBI:100128927 ∙ OMIM:613915 ∙ HGNC:32550 ∙ Uniprot:B2RXF5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• lethal congenital contracture syndrome 6 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lethal congenital contracture syndrome 6	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	Musculoskeletal	25055871

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZBTB42 gene.

• Inborn genetic diseases (21 variants)
• not provided (10 variants)
• Lethal congenital contracture syndrome 6 (3 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB42 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				2	5	7
missense			23		3	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	8

Variants in ZBTB42

This is a list of pathogenic ClinVar variants found in the ZBTB42 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-104801242-A-G		Lethal congenital contracture syndrome 6	Benign (Dec 05, 2021)
14-104801277-C-T		not specified	Uncertain significance (Jan 26, 2022)
14-104801324-G-C		not specified	Uncertain significance (Mar 16, 2022)
14-104801353-C-G		not specified	Uncertain significance (Jan 23, 2024)
14-104801362-C-G		not specified	Uncertain significance (Apr 07, 2023)
14-104801378-C-A		not specified	Uncertain significance (Mar 11, 2022)
14-104801384-A-C		not specified	Uncertain significance (Apr 07, 2023)
14-104801401-C-T			Likely benign (May 14, 2018)
14-104801456-C-T		not specified	Uncertain significance (Jan 23, 2023)
14-104801507-T-C		not specified	Uncertain significance (Nov 10, 2022)
14-104801530-C-A		ZBTB42-related disorder	Likely benign (Mar 30, 2019)
14-104801588-G-A		not specified	Uncertain significance (May 27, 2022)
14-104801597-G-A		ZBTB42-related disorder	Benign (May 05, 2021)
14-104801669-A-C		not specified	Uncertain significance (Jan 09, 2023)
14-104801767-G-A			Benign (Nov 13, 2018)
14-104801781-G-A		not specified	Uncertain significance (Mar 06, 2023)
14-104801796-G-A		not specified	Uncertain significance (Jan 04, 2024)
14-104801808-C-T		not specified	Uncertain significance (Dec 07, 2021)
14-104801835-G-T		not specified	Uncertain significance (Feb 15, 2023)
14-104801891-G-A		Lethal congenital contracture syndrome 6	Benign (Dec 05, 2021)
14-104801904-G-A		not specified	Uncertain significance (May 17, 2023)
14-104801934-C-T		not specified	Likely benign (Oct 13, 2023)
14-104802023-C-T		not specified	Uncertain significance (Nov 08, 2022)
14-104802045-G-A		not specified	Uncertain significance (Nov 21, 2022)
14-104802076-C-A		ZBTB42-related disorder	Likely benign (Mar 21, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB42	protein_coding	protein_coding	ENST00000342537	1	4117

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.338	0.659	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	172	249	0.690	0.0000154	2682
Missense in Polyphen		48	91.052	0.52717		983
Synonymous	2.33	83	115	0.723	0.00000722	941
Loss of Function	2.57	3	13.0	0.231	9.27e-7	118

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. Specifically binds DNA and probably acts by recruiting chromatin remodeling multiprotein complexes. {ECO:0000250|UniProtKB:Q811H0}.

Intolerance Scores

• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.89

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.193

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb42

Zebrafish Information Network

• Gene name: zbtb42
• Affected structure: skeletal muscle cell
• Phenotype tag: abnormal
• Phenotype quality: atrophied

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;cellular response to DNA damage stimulus;muscle organ development
• Cellular component: nucleus;nucleoplasm;cytoplasm;plasma membrane
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding