ZNF420

zinc finger protein 420, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:37007857-37130368

Links

ENSG00000197050 ∙ NCBI:147923 ∙ OMIM:617216 ∙ HGNC:20649 ∙ Uniprot:Q8TAQ5 ∙ 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 ZNF420 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF420 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			24			24
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in ZNF420

This is a list of pathogenic ClinVar variants found in the ZNF420 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-37091027-C-A		not specified	Uncertain significance (Mar 25, 2024)
19-37091082-G-C		not specified	Uncertain significance (Jul 05, 2023)
19-37127229-G-A		not specified	Uncertain significance (Mar 16, 2024)
19-37127241-T-C		not specified	Uncertain significance (Jun 16, 2024)
19-37127278-T-C		not specified	Uncertain significance (Dec 08, 2023)
19-37127353-A-G		Breast ductal adenocarcinoma	Uncertain significance (Jul 20, 2015)
19-37127399-G-T		not specified	Uncertain significance (Mar 07, 2024)
19-37127512-A-G		not specified	Uncertain significance (May 03, 2023)
19-37127598-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-37127754-G-C		not specified	Uncertain significance (Jun 09, 2022)
19-37127812-C-T		not specified	Uncertain significance (Nov 12, 2021)
19-37127822-G-C		not specified	Uncertain significance (May 25, 2022)
19-37127885-G-C		not specified	Uncertain significance (Nov 08, 2022)
19-37127898-G-A		not specified	Uncertain significance (Mar 27, 2023)
19-37127967-C-A		not specified	Uncertain significance (Jan 20, 2023)
19-37128067-G-C		not specified	Uncertain significance (May 15, 2024)
19-37128363-C-T		not specified	Uncertain significance (Oct 06, 2021)
19-37128391-G-A		not specified	Uncertain significance (Aug 12, 2021)
19-37128613-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-37128616-G-A		not specified	Uncertain significance (Sep 22, 2023)
19-37128632-A-G		not specified	Uncertain significance (Dec 14, 2021)
19-37128661-A-C		not specified	Uncertain significance (Dec 14, 2021)
19-37128688-A-G		not specified	Uncertain significance (Sep 27, 2022)
19-37128708-C-G		not specified	Uncertain significance (Mar 18, 2024)
19-37128767-T-A			Uncertain significance (Jan 27, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF420	protein_coding	protein_coding	ENST00000337995	3	122458

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.86e-11	0.609	125681	0	67	125748	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	273	369	0.741	0.0000184	4569
Missense in Polyphen		35	52.061	0.67228		498
Synonymous	0.226	117	120	0.974	0.00000558	1193
Loss of Function	1.44	21	29.4	0.714	0.00000169	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.000115	0.000109
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000353	0.000334
Middle Eastern	0.000115	0.000109
South Asian	0.000310	0.000294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;TP53 Regulates Transcription of Genes Involved in Cytochrome C Release;Transcriptional Regulation by TP53 (Consensus)

Intolerance Scores

• loftool: 0.795
• rvis_EVS: -1.02
• rvis_percentile_EVS: 7.94

Haploinsufficiency Scores

• pHI: 0.208
• hipred: N
• hipred_score: 0.455
• ghis: 0.620

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp420

Gene ontology

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