ZNF470

zinc finger protein 470, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:56567468-56588911

Links

ENSG00000197016 ∙ NCBI:388566 ∙ ∙ HGNC:22220 ∙ Uniprot:Q6ECI4 ∙ 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 ZNF470 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF470 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			55	3		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	3	0

Variants in ZNF470

This is a list of pathogenic ClinVar variants found in the ZNF470 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-56574400-G-A		not specified	Uncertain significance (Aug 30, 2021)
19-56574415-G-A		not specified	Uncertain significance (May 30, 2023)
19-56574445-G-C		not specified	Uncertain significance (Dec 14, 2022)
19-56574452-T-A		not specified	Uncertain significance (Jan 02, 2024)
19-56574460-G-T		not specified	Uncertain significance (Jul 15, 2021)
19-56574479-A-T		not specified	Uncertain significance (Jun 12, 2023)
19-56574484-G-A		not specified	Uncertain significance (Nov 09, 2024)
19-56574490-T-A		not specified	Uncertain significance (Jun 26, 2023)
19-56574500-A-G		not specified	Uncertain significance (Sep 20, 2023)
19-56574646-A-G		not specified	Uncertain significance (Apr 05, 2023)
19-56574658-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-56574690-C-G		not specified	Likely benign (May 31, 2023)
19-56574700-A-G		not specified	Uncertain significance (May 04, 2023)
19-56574710-G-A		not specified	Likely benign (Apr 28, 2023)
19-56574716-A-G		not specified	Uncertain significance (Oct 07, 2024)
19-56574728-G-A		not specified	Uncertain significance (Nov 07, 2022)
19-56576753-C-G		not specified	Uncertain significance (Jun 30, 2022)
19-56576843-C-A		not specified	Uncertain significance (Sep 30, 2024)
19-56576892-C-T		not specified	Uncertain significance (Jun 06, 2023)
19-56576893-A-G		not specified	Uncertain significance (Jun 18, 2021)
19-56576900-G-T		not specified	Uncertain significance (Jun 10, 2024)
19-56577014-G-A		not specified	Likely benign (Aug 16, 2021)
19-56577015-G-A		not specified	Uncertain significance (Feb 06, 2024)
19-56577052-G-A		not specified	Uncertain significance (Jul 16, 2024)
19-56577061-C-T		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF470	protein_coding	protein_coding	ENST00000330619	4	21400

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.68e-19	0.000830	125581	1	161	125743	0.000644

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.979	428	375	1.14	0.0000178	4776
Missense in Polyphen		199	172.61	1.1529		2198
Synonymous	0.318	122	127	0.964	0.00000607	1256
Loss of Function	-0.573	27	24.0	1.13	0.00000115	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000717	0.000710
Ashkenazi Jewish	0.00	0.00
East Asian	0.000507	0.000489
Finnish	0.00131	0.00129
European (Non-Finnish)	0.000660	0.000651
Middle Eastern	0.000507	0.000489
South Asian	0.000933	0.000882
Other	0.000655	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: 0.655
• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.8

Haploinsufficiency Scores

• pHI: 0.171
• hipred: N
• hipred_score: 0.146
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0948

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, DNA-templated
• Cellular component: nucleoplasm;nuclear body
• Molecular function: DNA binding;metal ion binding