ZXDA

protein-coding

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

Gene summary

This gene encodes one of two duplicated zinc finger genes on chromosome Xp11. This gene is the telomeric copy; GeneID 158586 ZXDB is the more centromeric copy. The two genes have 98% nucleotide sequence similarity, and the predicted proteins contain 10 tandem zinc finger motifs. [provided by RefSeq, Nov 2009]

MANE transcript

NM_007156.5

Inheritance

—

ClinVar variants

U:77B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chrX:57,905,430-57,910,458

External References & Databases

Ensembl (ENSG00000198205)

Transcript & Mutation Effects

hg38 • Region Span ~5.0 kb

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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 ZXDA variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007156.5. 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				4 clinvar		4
missense			76 clinvar	12 clinvar		88
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	77	16	0	93

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_007156.5	RefSeq	NP_009087.1	1	MANE Select
ENST00000358697.6	Ensembl	ENSP00000351530.4	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
positive regulation of transcription, DNA-templated

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358697
Coding exons: 1
Length: 5204
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	0.193	289	298	0.969	0.0000245	5154
Missense (PolyPhen)		127	149.15	0.8515		2648
Synonymous	-0.659	154	144	1.07	0.0000133	1703
Loss of Function	1.33	5	9.41	0.531	5.99e-7	189

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:0000269|PubMed:17493635}.;

Recessive Scores

pRec: 0.0978

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: N
Indispensability score: 0.0747

Gene Damage Prediction

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