ZNF239

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

Basic information

Region (hg38): 10:43556344-43574618

Links

ENSG00000196793 ∙ ∙ OMIM:601069 ∙ HGNC:13031 ∙ Uniprot:Q16600 ∙ 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 ZNF239 gene.

• not_specified (56 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF239 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001099282.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			51	5		56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	5	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF239	protein_coding	protein_coding	ENST00000306006	1	18275

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.05e-7	0.459	125520	0	96	125616	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.178	231	239	0.968	0.0000123	3078
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00104
Ashkenazi Jewish	0.00	0.00
East Asian	0.000719	0.000707
Finnish	0.000650	0.000647
European (Non-Finnish)	0.000292	0.000290
Middle Eastern	0.000719	0.000707
South Asian	0.000196	0.000196
Other	0.000327	0.000327

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.123
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.825

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp239

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• 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;protein binding;metal ion binding