ZXDB

zinc finger X-linked duplicated B, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): X:57592011-57597477

Links

ENSG00000198455 ∙ NCBI:158586 ∙ OMIM:300236 ∙ HGNC:13199 ∙ Uniprot:P98169 ∙ 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 ZXDB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZXDB 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			67	4		71
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	67	12	0

Variants in ZXDB

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

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

Position	Type	Phenotype	Significance	ClinVar
X-57592067-C-T		not specified	Uncertain significance (Feb 13, 2024)
X-57592118-G-A		not specified	Uncertain significance (May 30, 2022)
X-57592166-C-T		not specified	Uncertain significance (Oct 30, 2024)
X-57592167-C-T		not specified	Uncertain significance (Jan 23, 2023)
X-57592169-A-C		not specified	Uncertain significance (Jan 30, 2024)
X-57592173-G-A		not specified	Uncertain significance (May 30, 2023)
X-57592199-C-G		not specified	Uncertain significance (Mar 02, 2023)
X-57592248-G-C		not specified	Uncertain significance (Aug 02, 2023)
X-57592248-G-T		not specified	Uncertain significance (Dec 22, 2024)
X-57592251-G-A		not specified	Uncertain significance (Jan 05, 2022)
X-57592270-G-C		not specified	Conflicting classifications of pathogenicity (May 14, 2024)
X-57592280-A-C			Likely benign (Feb 01, 2023)
X-57592283-G-C			Likely benign (Feb 01, 2023)
X-57592292-A-G		not specified	Likely benign (Apr 29, 2024)
X-57592292-AGCGGCGGCGGCG-A			Likely benign (Jun 01, 2023)
X-57592305-G-T		not specified	Uncertain significance (Aug 17, 2021)
X-57592315-C-T			Likely benign (Feb 01, 2023)
X-57592358-G-T		not specified	Uncertain significance (Feb 18, 2025)
X-57592371-G-C		not specified	Uncertain significance (Sep 06, 2022)
X-57592376-G-A		not specified	Uncertain significance (May 18, 2023)
X-57592385-G-A		not specified	Likely benign (May 18, 2023)
X-57592399-G-T		not specified	Uncertain significance (Jan 05, 2022)
X-57592419-G-T		not specified	Uncertain significance (May 27, 2022)
X-57592432-G-C		not specified	Uncertain significance (Mar 03, 2025)
X-57592446-G-T		not specified	Uncertain significance (Sep 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZXDB	protein_coding	protein_coding	ENST00000374888	1	5638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.953	0.0472	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.964	228	273	0.836	0.0000202	5194
Missense in Polyphen		15	69.817	0.21485		1322
Synonymous	-2.20	152	121	1.25	0.00000961	1699
Loss of Function	2.87	0	9.58	0.00	6.09e-7	199

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: Cooperates with CIITA to promote transcription of MHC class I and MHC class II genes. {ECO:0000250}.

Recessive Scores

• pRec: 0.0994

Haploinsufficiency Scores

• pHI: 0.0626
• hipred: N
• hipred_score: 0.380
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.351

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zxdb

Gene ontology

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