ZNF471

zinc finger protein 471, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:56507850-56530221

Links

ENSG00000196263 ∙ NCBI:57573 ∙ OMIM:620162 ∙ HGNC:23226 ∙ Uniprot:Q9BX82 ∙ 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 ZNF471 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF471 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			49	4		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	5	0

Variants in ZNF471

This is a list of pathogenic ClinVar variants found in the ZNF471 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-56516366-T-A		not specified	Uncertain significance (Jul 26, 2024)
19-56518535-C-A		not specified	Uncertain significance (Feb 27, 2024)
19-56524373-G-C		not specified	Likely benign (Mar 25, 2024)
19-56524456-T-A		not specified	Uncertain significance (Oct 01, 2024)
19-56524499-A-T		not specified	Uncertain significance (Aug 12, 2021)
19-56524513-A-G		not specified	Uncertain significance (Dec 21, 2023)
19-56524567-G-A		not specified	Uncertain significance (Aug 02, 2023)
19-56524641-A-G		not specified	Uncertain significance (Nov 15, 2024)
19-56524649-A-G		not specified	Uncertain significance (Mar 10, 2025)
19-56524694-T-G		not specified	Uncertain significance (Jul 20, 2021)
19-56524750-A-C		not specified	Uncertain significance (Jun 11, 2021)
19-56524789-A-C		not specified	Uncertain significance (Nov 21, 2022)
19-56524809-C-T		not specified	Uncertain significance (Oct 06, 2021)
19-56524811-C-A		not specified	Uncertain significance (Feb 24, 2025)
19-56524816-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-56524837-C-A		not specified	Uncertain significance (Apr 12, 2022)
19-56524858-G-A		not specified	Uncertain significance (Jan 05, 2022)
19-56524866-T-G		not specified	Uncertain significance (Nov 07, 2023)
19-56524888-G-A		not specified	Likely benign (Nov 24, 2024)
19-56524923-G-A		not specified	Uncertain significance (Mar 06, 2025)
19-56524935-T-C		not specified	Uncertain significance (Jan 18, 2025)
19-56524959-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-56524993-A-G			Likely benign (Dec 01, 2022)
19-56525020-A-G		not specified	Uncertain significance (Aug 28, 2024)
19-56525034-T-C		not specified	Uncertain significance (Sep 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF471	protein_coding	protein_coding	ENST00000308031	4	22379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000609	0.974	125572	0	168	125740	0.000668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.986	273	323	0.846	0.0000149	4204
Missense in Polyphen		152	171.76	0.88495		2178
Synonymous	0.677	98	107	0.917	0.00000507	1045
Loss of Function	2.04	12	22.4	0.535	0.00000101	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000788	0.000782
Ashkenazi Jewish	0.00	0.00
East Asian	0.000470	0.000435
Finnish	0.000437	0.000416
European (Non-Finnish)	0.00107	0.000985
Middle Eastern	0.000470	0.000435
South Asian	0.000459	0.000457
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.738
• rvis_EVS: 1.18
• rvis_percentile_EVS: 92.75

Haploinsufficiency Scores

• pHI: 0.201
• hipred: N
• hipred_score: 0.168
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.483

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp78

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