ZNF454

zinc finger protein 454, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 5:178941191-178966433

Links

ENSG00000178187 ∙ NCBI:285676 ∙ ∙ HGNC:21200 ∙ Uniprot:Q8N9F8 ∙ 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 ZNF454 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF454 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in ZNF454

This is a list of pathogenic ClinVar variants found in the ZNF454 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-178946398-C-G		not specified	Uncertain significance (Feb 27, 2023)
5-178946469-C-A		not specified	Uncertain significance (Feb 13, 2024)
5-178946918-A-G		not specified	Uncertain significance (May 25, 2022)
5-178946940-A-T		not specified	Uncertain significance (Jul 14, 2021)
5-178946981-G-C		not specified	Uncertain significance (Dec 28, 2023)
5-178964705-C-T		not specified	Uncertain significance (Oct 12, 2021)
5-178964720-G-C		not specified	Uncertain significance (Mar 29, 2022)
5-178964732-A-G		not specified	Uncertain significance (Jun 10, 2024)
5-178964807-A-T		not specified	Uncertain significance (Jun 17, 2022)
5-178964877-C-G		not specified	Uncertain significance (Apr 08, 2024)
5-178965186-A-G		not specified	Uncertain significance (Jun 29, 2022)
5-178965210-A-G		not specified	Uncertain significance (Nov 17, 2023)
5-178965248-A-T		not specified	Uncertain significance (Mar 25, 2024)
5-178965258-T-C		not specified	Uncertain significance (Nov 08, 2021)
5-178965369-A-G		not specified	Uncertain significance (Oct 06, 2021)
5-178965495-C-G		not specified	Uncertain significance (Mar 28, 2023)
5-178965513-C-G		not specified	Uncertain significance (Nov 10, 2022)
5-178965565-T-A		not specified	Uncertain significance (Jul 09, 2021)
5-178965566-G-C		not specified	Uncertain significance (Jun 29, 2023)
5-178965657-A-G		not specified	Uncertain significance (Apr 09, 2024)
5-178965896-T-G		not specified	Uncertain significance (Jul 27, 2022)
5-178965902-A-G		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF454	protein_coding	protein_coding	ENST00000320129	4	25243

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000364	0.949	125681	0	67	125748	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	216	276	0.782	0.0000131	3510
Missense in Polyphen		72	108.84	0.66152		1383
Synonymous	0.0646	97	97.8	0.992	0.00000498	899
Loss of Function	1.84	12	21.1	0.568	0.00000114	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000773	0.000771
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000273	0.000272
South Asian	0.000229	0.000229
Other	0.000660	0.000652

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: 0.816
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.162
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp454

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