ZNF429

zinc finger protein 429, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:21496681-21556270

Links

ENSG00000197013 ∙ NCBI:353088 ∙ ∙ HGNC:20817 ∙ Uniprot:Q86V71 ∙ 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 ZNF429 gene.

• Inborn genetic diseases (26 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF429 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				4		4
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	5	0

Variants in ZNF429

This is a list of pathogenic ClinVar variants found in the ZNF429 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-21529713-G-A		not specified	Uncertain significance (Dec 18, 2023)
19-21529776-T-C		not specified	Uncertain significance (Jul 27, 2022)
19-21530643-C-A		not specified	Uncertain significance (Jul 26, 2022)
19-21536360-T-C		not specified	Uncertain significance (Dec 31, 2023)
19-21536369-C-T		not specified	Likely benign (Feb 28, 2023)
19-21536429-T-C		not specified	Uncertain significance (Apr 17, 2023)
19-21536430-A-G		not specified	Uncertain significance (Dec 18, 2023)
19-21536487-A-G		not specified	Uncertain significance (Apr 07, 2023)
19-21536531-G-A		not specified	Uncertain significance (Jul 12, 2023)
19-21536546-A-G		not specified	Uncertain significance (Dec 01, 2022)
19-21536556-C-T		not specified	Uncertain significance (May 03, 2023)
19-21536703-C-A		not specified	Uncertain significance (Nov 17, 2022)
19-21536715-G-C		not specified	Uncertain significance (Nov 18, 2022)
19-21536792-C-T		not specified	Uncertain significance (Jan 19, 2024)
19-21537004-AT-A			Uncertain significance (Sep 08, 2023)
19-21537024-G-A		not specified	Uncertain significance (May 11, 2022)
19-21537057-A-C		not specified	Uncertain significance (May 27, 2022)
19-21537086-G-A		not specified	Uncertain significance (Aug 02, 2022)
19-21537107-T-C		not specified	Uncertain significance (Oct 05, 2023)
19-21537159-A-G		not specified	Uncertain significance (Oct 26, 2022)
19-21537168-A-G		not specified	Uncertain significance (Dec 27, 2023)
19-21537213-A-G		not specified	Uncertain significance (Dec 27, 2022)
19-21537356-A-G		not specified	Uncertain significance (May 31, 2023)
19-21537393-A-G		not specified	Uncertain significance (Jan 18, 2022)
19-21537444-G-A		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF429	protein_coding	protein_coding	ENST00000358491	4	59589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000405	0.233	125578	0	21	125599	0.0000836

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.994	392	340	1.15	0.0000162	4425
Missense in Polyphen		106	97.696	1.085		1423
Synonymous	-0.537	124	117	1.06	0.00000524	1188
Loss of Function	-0.481	6	4.86	1.24	2.06e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000312	0.0000312
Ashkenazi Jewish	0.000404	0.000397
East Asian	0.0000555	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000924	0.0000880
Middle Eastern	0.0000555	0.0000544
South Asian	0.000148	0.000131
Other	0.000167	0.000163

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: 0.791
• rvis_EVS: 1.56
• rvis_percentile_EVS: 95.66

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.104

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;metal ion binding