ZNF474

zinc finger protein 474, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 5:122129546-122182658

Links

ENSG00000164185 ∙ NCBI:133923 ∙ ∙ HGNC:23245 ∙ Uniprot:Q6S9Z5 ∙ 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 ZNF474 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF474 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					1	1
missense			26	1	4	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	5

Variants in ZNF474

This is a list of pathogenic ClinVar variants found in the ZNF474 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-122152000-G-A		not specified	Uncertain significance (Nov 10, 2021)
5-122152070-T-A		not specified	Uncertain significance (Aug 16, 2022)
5-122152156-A-G		not specified	Uncertain significance (Apr 15, 2024)
5-122152163-C-T		not specified	Uncertain significance (Jul 27, 2022)
5-122152169-A-G		not specified	Uncertain significance (Jan 03, 2022)
5-122152177-C-A		not specified	Uncertain significance (Dec 04, 2024)
5-122152177-C-G		not specified	Uncertain significance (Sep 03, 2024)
5-122152178-C-A		not specified	Uncertain significance (Feb 23, 2023)
5-122152221-A-G		not specified	Likely benign (Sep 10, 2024)
5-122152243-C-A		not specified	Uncertain significance (Aug 14, 2024)
5-122152250-T-C		not specified	Uncertain significance (Jan 23, 2023)
5-122152254-G-A			Benign (Apr 05, 2018)
5-122152258-C-T		not specified	Uncertain significance (Sep 03, 2024)
5-122152259-G-A			Benign (Apr 05, 2018)
5-122152259-G-T		not specified	Uncertain significance (Jan 06, 2023)
5-122152264-C-T		not specified	Uncertain significance (Nov 17, 2023)
5-122152276-G-T			Benign (Feb 26, 2018)
5-122152316-T-C		not specified	Uncertain significance (Nov 15, 2024)
5-122152419-C-A		not specified	Uncertain significance (Mar 29, 2023)
5-122152424-G-A		not specified	Uncertain significance (Nov 08, 2024)
5-122152426-G-A		not specified	Uncertain significance (Feb 06, 2023)
5-122152507-C-T		not specified	Uncertain significance (May 24, 2024)
5-122152562-G-T		not specified	Uncertain significance (Nov 04, 2023)
5-122152585-T-C			Benign (Apr 05, 2018)
5-122152606-A-T		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF474	protein_coding	protein_coding	ENST00000296600	1	50105

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000718	0.772	125687	0	58	125745	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.53	249	190	1.31	0.00000940	2366
Missense in Polyphen		63	49.927	1.2618		664
Synonymous	-2.16	96	72.6	1.32	0.00000364	730
Loss of Function	1.01	6	9.34	0.642	5.75e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000359	0.000358
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000361	0.000360
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0679

Intolerance Scores

• loftool: 0.689
• rvis_EVS: 1.98
• rvis_percentile_EVS: 97.61

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0274

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp474

Gene ontology

• Molecular function: nucleic acid binding;metal ion binding