ZXDB

protein-coding

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

Gene summary

The ZXDB gene is one of a pair of duplicated zinc finger genes on chromosome Xp11.21 (Greig et al., 1993 [PubMed 8268913]); see also ZXDA (MIM 300235).[supplied by OMIM, Jul 2010]

MANE transcript

NM_007157.4

Inheritance

—

ClinVar variants

U:107B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:57,592,011-57,597,477

External References & Databases

Ensembl (ENSG00000198455)

Transcript & Mutation Effects

hg38 • Region Span ~5.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZXDB variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007157.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				7 clinvar		7
missense			106 clinvar	7 clinvar		113
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	107	14	0	121

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007157.4	RefSeq	NP_009088.1	1	MANE Select
ENST00000374888.3	Ensembl	ENSP00000364023.1	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
biological_process

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
molecular_function
nucleic acid binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374888
Coding exons: 1
Length: 5638
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.964	228	273	0.836	0.0000202	5194
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.351

Gene Damage Prediction

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