ZNF439

zinc finger protein 439, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:11848726-11883750

Links

ENSG00000171291 ∙ NCBI:90594 ∙ ∙ HGNC:20873 ∙ Uniprot:Q8NDP4 ∙ 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 ZNF439 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF439 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			27	7		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	7	0

Variants in ZNF439

This is a list of pathogenic ClinVar variants found in the ZNF439 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11866278-A-G		not specified	Uncertain significance (Jul 12, 2022)
19-11866282-T-A		not specified	Uncertain significance (Jul 12, 2022)
19-11866313-T-A		not specified	Likely benign (Jan 04, 2024)
19-11866560-A-G		not specified	Uncertain significance (Dec 12, 2024)
19-11866592-C-A		not specified	Uncertain significance (Mar 31, 2024)
19-11867329-A-G		not specified	Uncertain significance (Dec 28, 2022)
19-11867400-A-G		not specified	Likely benign (Jul 12, 2023)
19-11867480-G-A		not specified	Uncertain significance (Feb 12, 2025)
19-11867497-C-T		not specified	Likely benign (Nov 22, 2024)
19-11867523-G-A		not specified	Uncertain significance (Dec 30, 2024)
19-11867557-C-T		not specified	Likely benign (Dec 01, 2022)
19-11867588-G-T		not specified	Likely benign (Oct 03, 2022)
19-11867596-A-C		not specified	Uncertain significance (Oct 19, 2024)
19-11867598-G-C		not specified	Uncertain significance (Oct 19, 2024)
19-11867623-C-T		not specified	Uncertain significance (Nov 20, 2024)
19-11867662-A-G		not specified	Uncertain significance (Dec 31, 2024)
19-11867670-A-C		not specified	Uncertain significance (Apr 27, 2024)
19-11867692-A-C		not specified	Uncertain significance (Dec 07, 2024)
19-11867725-G-C		not specified	Uncertain significance (Jan 30, 2024)
19-11867736-T-G		not specified	Uncertain significance (Dec 19, 2022)
19-11867791-C-T		not specified	Uncertain significance (Nov 09, 2024)
19-11867941-G-T		not specified	Likely benign (Mar 14, 2023)
19-11867947-T-C		not specified	Likely benign (Jul 19, 2023)
19-11867950-G-C		not specified	Uncertain significance (Jul 05, 2024)
19-11867973-G-A		not specified	Uncertain significance (Oct 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF439	protein_coding	protein_coding	ENST00000304030	3	35025

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0122	0.663	124582	23	1104	125709	0.00449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.481	279	257	1.08	0.0000124	3315
Missense in Polyphen		67	83.801	0.79951		1149
Synonymous	0.596	81	88.1	0.919	0.00000416	864
Loss of Function	0.501	3	4.09	0.733	1.74e-7	49

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0657	0.0664
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000281	0.000281
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.705
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.09

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.112
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.142

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding