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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in ZNF239

This is a list of pathogenic ClinVar variants found in the ZNF239 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-43556707-C-T		not specified	Likely benign (Nov 21, 2023)
10-43556712-A-C		not specified	Uncertain significance (Apr 12, 2024)
10-43556720-T-C		not specified	Uncertain significance (May 24, 2024)
10-43556729-G-A		not specified	Uncertain significance (Jan 23, 2024)
10-43556776-T-G		not specified	Uncertain significance (Sep 01, 2021)
10-43556829-T-A		not specified	Uncertain significance (May 12, 2024)
10-43556875-G-T		not specified	Uncertain significance (Dec 17, 2023)
10-43556917-G-C		not specified	Uncertain significance (Aug 02, 2021)
10-43556984-G-A		not specified	Uncertain significance (Dec 28, 2023)
10-43557004-C-T		not specified	Uncertain significance (Dec 14, 2022)
10-43557040-T-A		not specified	Uncertain significance (Oct 27, 2021)
10-43557089-G-A		not specified	Uncertain significance (Dec 01, 2022)
10-43557098-A-C		not specified	Uncertain significance (Jul 19, 2022)
10-43557148-C-T		not specified	Uncertain significance (Feb 17, 2024)
10-43557151-T-A		not specified	Uncertain significance (Oct 03, 2022)
10-43557185-C-T		not specified	Uncertain significance (Aug 31, 2022)
10-43557199-T-C		not specified	Uncertain significance (Oct 29, 2021)
10-43557218-C-T		not specified	Uncertain significance (Jan 23, 2023)
10-43557280-T-C		not specified	Uncertain significance (Jun 18, 2021)
10-43557296-G-C		not specified	Uncertain significance (Sep 17, 2021)
10-43557318-C-G		not specified	Uncertain significance (Feb 06, 2024)
10-43557428-G-C		not specified	Likely benign (Jun 10, 2024)
10-43557432-G-C		not specified	Uncertain significance (Dec 30, 2023)
10-43557547-G-C		not specified	Uncertain significance (Jan 23, 2023)
10-43557604-C-A		not specified	Uncertain significance (Feb 06, 2024)

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