ZFP2

ZFP2 zinc finger protein, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 5:178895897-178933212

Links

ENSG00000198939 ∙ NCBI:80108 ∙ ∙ HGNC:26138 ∙ Uniprot:Q6ZN57 ∙ 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 ZFP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFP2 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			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	0	0

Variants in ZFP2

This is a list of pathogenic ClinVar variants found in the ZFP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-178931323-G-A		not specified	Uncertain significance (Mar 29, 2024)
5-178931376-A-C		not specified	Uncertain significance (Jul 09, 2021)
5-178931413-G-C		not specified	Uncertain significance (May 28, 2024)
5-178931428-A-C		not specified	Uncertain significance (Mar 04, 2024)
5-178931501-C-A		not specified	Uncertain significance (Sep 14, 2022)
5-178931515-C-T		not specified	Uncertain significance (Apr 20, 2023)
5-178931520-G-T		not specified	Uncertain significance (Oct 25, 2022)
5-178931614-A-G		not specified	Uncertain significance (Jan 04, 2022)
5-178931618-A-G		not specified	Uncertain significance (May 01, 2022)
5-178931660-C-A		not specified	Uncertain significance (Mar 11, 2022)
5-178931695-A-G		not specified	Uncertain significance (Jun 09, 2022)
5-178931702-A-G		not specified	Uncertain significance (Dec 18, 2023)
5-178931711-A-G		not specified	Uncertain significance (Jul 25, 2023)
5-178931716-T-C		not specified	Uncertain significance (Dec 22, 2023)
5-178931720-G-A		not specified	Uncertain significance (Jan 03, 2024)
5-178931828-A-G		not specified	Uncertain significance (Jun 21, 2023)
5-178931846-G-A		not specified	Uncertain significance (Mar 15, 2024)
5-178931857-G-A		not specified	Uncertain significance (Nov 09, 2022)
5-178931893-G-C		not specified	Uncertain significance (Jan 16, 2024)
5-178931902-A-G		not specified	Uncertain significance (Jan 02, 2024)
5-178931987-A-G		not specified	Uncertain significance (Oct 06, 2021)
5-178932035-C-G		not specified	Uncertain significance (Aug 02, 2021)
5-178932074-G-C		not specified	Uncertain significance (Mar 17, 2023)
5-178932077-T-G		not specified	Uncertain significance (Apr 27, 2024)
5-178932089-T-A		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFP2	protein_coding	protein_coding	ENST00000361362	1	37319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.66e-17	0.000905	125485	0	259	125744	0.00103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0323	243	244	0.994	0.0000116	3080
Missense in Polyphen		113	120.88	0.93479		1498
Synonymous	0.497	76	81.7	0.930	0.00000390	805
Loss of Function	-0.994	23	18.4	1.25	0.00000116	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00452	0.00452
Ashkenazi Jewish	0.00	0.00
East Asian	0.00141	0.00141
Finnish	0.000555	0.000554
European (Non-Finnish)	0.000423	0.000404
Middle Eastern	0.00141	0.00141
South Asian	0.000425	0.000425
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcription factor involved in neuronal differentiation and/or phenotypic maintenance. {ECO:0000250}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.919
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.07

Haploinsufficiency Scores

• pHI: 0.204
• hipred: N
• hipred_score: 0.170
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.763

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp2

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;protein binding;metal ion binding