ZNF439

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

Basic information

Region (hg38): 19:11848726-11883750

Links

ENSG00000171291NCBI:90594HGNC:20873Uniprot:Q8NDP4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
7
clinvar
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)2300573
19-11866282-T-A not specified Uncertain significance (Jul 12, 2022)2300574
19-11866313-T-A not specified Likely benign (Jan 04, 2024)3195772
19-11866560-A-G not specified Uncertain significance (Dec 12, 2024)3820921
19-11866592-C-A not specified Uncertain significance (Mar 31, 2024)3335784
19-11867329-A-G not specified Uncertain significance (Dec 28, 2022)2340558
19-11867400-A-G not specified Likely benign (Jul 12, 2023)2601293
19-11867480-G-A not specified Uncertain significance (Feb 12, 2025)3820925
19-11867497-C-T not specified Likely benign (Nov 22, 2024)3475918
19-11867523-G-A not specified Uncertain significance (Dec 30, 2024)3820924
19-11867557-C-T not specified Likely benign (Dec 01, 2022)2331111
19-11867588-G-T not specified Likely benign (Oct 03, 2022)2381686
19-11867596-A-C not specified Uncertain significance (Oct 19, 2024)3475913
19-11867598-G-C not specified Uncertain significance (Oct 19, 2024)3475914
19-11867623-C-T not specified Uncertain significance (Nov 20, 2024)3475917
19-11867662-A-G not specified Uncertain significance (Dec 31, 2024)3820920
19-11867670-A-C not specified Uncertain significance (Apr 27, 2024)3335786
19-11867692-A-C not specified Uncertain significance (Dec 07, 2024)3475919
19-11867725-G-C not specified Uncertain significance (Jan 30, 2024)3195773
19-11867736-T-G not specified Uncertain significance (Dec 19, 2022)2208015
19-11867791-C-T not specified Uncertain significance (Nov 09, 2024)3475909
19-11867941-G-T not specified Likely benign (Mar 14, 2023)2454355
19-11867947-T-C not specified Likely benign (Jul 19, 2023)2612519
19-11867950-G-C not specified Uncertain significance (Jul 05, 2024)3475915
19-11867973-G-A not specified Uncertain significance (Oct 17, 2024)3475916

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ZNF439protein_codingprotein_codingENST00000304030 335025
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01220.6631245822311041257090.00449
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4812792571.080.00001243315
Missense in Polyphen6783.8010.799511149
Synonymous0.5968188.10.9190.00000416864
Loss of Function0.50134.090.7331.74e-749

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.06570.0664
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0002810.000281
Middle Eastern0.00005440.0000544
South Asian0.0001310.000131
Other0.001960.00196

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_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.142

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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