ZNF239

protein-coding

zinc finger protein 239, the group of Zinc fingers C2H2-type

Gene summary

MOK2 proteins are DNA- and RNA-binding proteins that are mainly associated with nuclear RNP components, including the nucleoli and extranucleolar structures (Arranz et al., 1997 [PubMed 9121460]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001099282.2

Inheritance

—

ClinVar variants

U:62B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr10:43,556,344-43,574,618

External References & Databases

Ensembl (ENSG00000196793)

Transcript & Mutation Effects

hg38 • Region Span ~18.3 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 ZNF239 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 66

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099282.2. 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						0
missense			62 clinvar	5 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	5	0	67

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 119 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001099282.2	RefSeq	NP_001092752.1	1	MANE Select
ENST00000374446.7	Ensembl	ENSP00000363569.1	1	MANE Select
NM_001099283.2	RefSeq	NP_001092753.1	1	Standard
NM_001099284.2	RefSeq	NP_001092754.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription repressor activity, RNA polymerase II-specific
DNA binding
RNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306006
Coding exons: 1
Length: 18275
Individuals with no LoFs: 125520
Homozygous LoFs: 0
Heterozygous LoFs: 96
Defined: 125616
p: 0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.178	231	239	0.968	0.0000123	3078
Missense (PolyPhen)		90	98.607	0.91271		1223
Synonymous	-0.199	90	87.6	1.03	0.00000456	806
Loss of Function	0.797	12	15.4	0.781	9.04e-7	203

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00045	0.00044	rare
Latino/Admixed American	0.00061	0.00061	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00072	0.00071	rare
Finnish	0.00065	0.00065	rare
European (Non-Finnish)	0.00029	0.00029	rare
South Asian	0.00020	0.00020	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.0810

Intolerance Scores

LoFtool: 0.885
RVIS EVS: -0.09
RVIS percentile EVS: 46.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.825

Gene Damage Prediction

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