ZXDC

protein-coding

ZXD family zinc finger C, the group of Zinc fingers C2H2-type

Gene summary

Enables C2H2 zinc finger domain binding activity; LRR domain binding activity; and transcription coactivator activity. Involved in positive regulation of DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_025112.5

Inheritance

—

ClinVar variants

U:164B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr3:126,437,601-126,475,891

External References & Databases

Ensembl (ENSG00000070476)

Transcript & Mutation Effects

hg38 • Region Span ~38.3 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 ZXDC variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 162

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025112.5. 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			3 clinvar			3
missense			157 clinvar	9 clinvar		166
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	164	9	0	173

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025112.5	RefSeq	NP_079388.3	10	MANE Select
ENST00000389709.8	Ensembl	ENSP00000374359.3	10	MANE Select
NM_001040653.4	RefSeq	NP_001035743.1	6	Standard
ENST00000336332.5	Ensembl	ENSP00000337694.5	6	Standard

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
LRR domain binding

Cellular Component

cellular_component
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389709
Coding exons: 10
Length: 38319
Individuals with no LoFs: 125530
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125561
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.38	357	438	0.815	0.0000239	5473
Missense (PolyPhen)		111	182.68	0.60762		2107
Synonymous	-1.04	206	188	1.10	0.0000112	1837
Loss of Function	1.54	18	26.6	0.678	0.00000136	312

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.000098	0.000098	rare
Other	0.00033	0.00033	rare

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:16600381, ECO:0000269|PubMed:17493635, ECO:0000269|PubMed:17696781}.;

Intolerance Scores

LoFtool: 0.679
RVIS EVS: -0.51
RVIS percentile EVS: 21.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.718

Gene Damage Prediction

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