ZNF404

zinc finger protein 404, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:43872364-43901385

Links

ENSG00000176222 ∙ NCBI:342908 ∙ ∙ HGNC:19417 ∙ Uniprot:Q494X3 ∙ 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 ZNF404 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF404 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				3		3
missense			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	28	5	0

Variants in ZNF404

This is a list of pathogenic ClinVar variants found in the ZNF404 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-43872574-C-G		not specified	Uncertain significance (Jun 22, 2023)
19-43872697-C-T		not specified	Uncertain significance (Jun 27, 2022)
19-43872707-C-T		not specified	Uncertain significance (Mar 18, 2024)
19-43872784-C-T		not specified	Uncertain significance (Sep 21, 2021)
19-43872965-C-G		not specified	Uncertain significance (Feb 17, 2024)
19-43873004-T-A		not specified	Uncertain significance (Mar 16, 2022)
19-43873007-T-C		not specified	Uncertain significance (Feb 28, 2023)
19-43873078-C-A		not specified	Uncertain significance (Jan 16, 2024)
19-43873228-C-T		not specified	Uncertain significance (Dec 21, 2022)
19-43873255-C-T		not specified	Likely benign (Dec 14, 2022)
19-43873357-A-G		not specified	Uncertain significance (Nov 07, 2023)
19-43873367-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-43873379-C-G		not specified	Uncertain significance (Sep 28, 2022)
19-43873441-A-G		not specified	Uncertain significance (Mar 26, 2024)
19-43873461-C-T			Likely benign (Feb 01, 2023)
19-43873504-T-G		not specified	Uncertain significance (Apr 25, 2023)
19-43873537-C-T		not specified	Uncertain significance (Jan 05, 2022)
19-43873546-G-T		not specified	Uncertain significance (Mar 23, 2023)
19-43873553-C-T		not specified	Uncertain significance (Aug 02, 2022)
19-43873585-G-C		not specified	Uncertain significance (Jan 22, 2024)
19-43873586-T-G		not specified	Uncertain significance (Aug 02, 2022)
19-43873587-A-G			Likely benign (Jan 01, 2023)
19-43873589-G-A		not specified	Uncertain significance (May 24, 2023)
19-43873648-C-T		not specified	Uncertain significance (May 11, 2022)
19-43873673-G-A		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF404	protein_coding	protein_coding	ENST00000587539	3	29023

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.68e-8	0.498	125253	0	135	125388	0.000538

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.992	243	291	0.836	0.0000139	3699
Missense in Polyphen		83	97.716	0.8494		1261
Synonymous	0.884	83	93.9	0.884	0.00000442	912
Loss of Function	0.975	14	18.5	0.756	8.99e-7	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00145	0.00143
Ashkenazi Jewish	0.000102	0.0000993
East Asian	0.00253	0.00250
Finnish	0.000660	0.000647
European (Non-Finnish)	0.000180	0.000176
Middle Eastern	0.00253	0.00250
South Asian	0.000333	0.000327
Other	0.000513	0.000492

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.
• Pathway: TCR (Consensus)

Haploinsufficiency Scores

• pHI: 0.0545
• hipred: N
• hipred_score: 0.112
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00146

Gene Damage Prediction

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

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