ZNF473

zinc finger protein 473, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:50025714-50053414

Links

ENSG00000142528 ∙ NCBI:25888 ∙ OMIM:617908 ∙ HGNC:23239 ∙ Uniprot:Q8WTR7 ∙ 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 ZNF473 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF473 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			35	5		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	8	0

Variants in ZNF473

This is a list of pathogenic ClinVar variants found in the ZNF473 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50039251-A-G		not specified	Uncertain significance (Sep 26, 2023)
19-50041741-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-50041811-C-T		not specified	Uncertain significance (Jul 19, 2022)
19-50044680-G-C		not specified	Uncertain significance (Jun 17, 2024)
19-50044786-G-A		not specified	Uncertain significance (Feb 06, 2023)
19-50044877-C-T		not specified	Uncertain significance (May 26, 2024)
19-50044912-A-G		not specified	Uncertain significance (Jun 06, 2023)
19-50044930-T-A		not specified	Uncertain significance (Jan 23, 2024)
19-50045003-G-A		not specified	Uncertain significance (Apr 28, 2023)
19-50045008-G-A		not specified	Uncertain significance (Jul 11, 2022)
19-50045009-A-G		not specified	Uncertain significance (Dec 28, 2022)
19-50045025-C-T			Likely benign (Sep 01, 2022)
19-50045104-A-C		not specified	Uncertain significance (Apr 13, 2022)
19-50045149-C-G		not specified	Uncertain significance (Jun 18, 2024)
19-50045203-G-A		not specified	Uncertain significance (Jun 10, 2024)
19-50045235-C-G		not specified	Uncertain significance (Sep 16, 2021)
19-50045321-A-T		not specified	Uncertain significance (May 01, 2024)
19-50045348-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-50045372-A-T		not specified	Uncertain significance (Mar 28, 2023)
19-50045387-C-A		not specified	Uncertain significance (Dec 20, 2021)
19-50045413-G-A		not specified	Uncertain significance (Oct 12, 2022)
19-50045471-C-T		not specified	Uncertain significance (Jun 19, 2024)
19-50045473-C-T		not specified	Uncertain significance (Oct 13, 2023)
19-50045474-G-A		not specified	Likely benign (Jan 10, 2022)
19-50045482-T-C		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF473	protein_coding	protein_coding	ENST00000595661	4	27701

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.262	0.738	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	395	492	0.803	0.0000275	5846
Missense in Polyphen		56	75.653	0.74022		771
Synonymous	0.274	183	188	0.975	0.0000114	1558
Loss of Function	3.85	7	29.7	0.236	0.00000152	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000370	0.000370
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.000359	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in histone 3'-end pre-mRNA processing by associating with U7 snRNP and interacting with SLBP/pre-mRNA complex. Increases histone 3'-end pre-mRNA processing but has no effect on U7 snRNP levels, when overexpressed. Required for cell cycle progression from G1 to S phases. {ECO:0000269|PubMed:11782445, ECO:0000269|PubMed:16714279, ECO:0000269|PubMed:16914750}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs;Metabolism of RNA;Processing of Capped Intronless Pre-mRNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;SLBP independent Processing of Histone Pre-mRNAs (Consensus)

Recessive Scores

• pRec: 0.0761

Intolerance Scores

• loftool: 0.513
• rvis_EVS: 1.61
• rvis_percentile_EVS: 95.91

Haploinsufficiency Scores

• pHI: 0.0530
• hipred: N
• hipred_score: 0.485
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.727

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp473

Gene ontology

• Biological process: regulation of transcription, DNA-templated;termination of RNA polymerase II transcription;mRNA 3'-end processing by stem-loop binding and cleavage;histone mRNA metabolic process
• Cellular component: nucleus;nucleoplasm;Cajal body
• Molecular function: DNA binding;protein binding;metal ion binding