ZFP42

ZFP42 zinc finger protein, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 4:187995771-188005046

Links

ENSG00000179059 ∙ NCBI:132625 ∙ OMIM:614572 ∙ HGNC:30949 ∙ Uniprot:Q96MM3 ∙ 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 ZFP42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFP42 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	1

Variants in ZFP42

This is a list of pathogenic ClinVar variants found in the ZFP42 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-188002833-C-T		not specified	Uncertain significance (Oct 31, 2022)
4-188002896-G-A		not specified	Uncertain significance (Nov 22, 2022)
4-188002994-C-G		not specified	Likely benign (Dec 28, 2022)
4-188002997-G-A		not specified	Uncertain significance (Aug 02, 2021)
4-188003060-A-G		not specified	Uncertain significance (May 31, 2023)
4-188003076-C-T		not specified	Uncertain significance (Nov 24, 2021)
4-188003088-C-A		not specified	Uncertain significance (Oct 29, 2021)
4-188003151-C-T		not specified	Uncertain significance (Nov 15, 2021)
4-188003196-A-G		not specified	Uncertain significance (Dec 01, 2022)
4-188003324-A-G		not specified	Uncertain significance (Mar 01, 2024)
4-188003327-A-C		not specified	Uncertain significance (Jan 09, 2024)
4-188003369-A-G		not specified	Uncertain significance (Nov 24, 2021)
4-188003544-G-T			Likely benign (Apr 20, 2018)
4-188003559-G-A		not specified	Uncertain significance (Mar 28, 2024)
4-188003581-G-A			Benign (Apr 20, 2018)
4-188003595-G-A		not specified	Uncertain significance (Mar 06, 2023)
4-188003618-G-A		not specified	Uncertain significance (Dec 02, 2021)
4-188003639-C-T		not specified	Uncertain significance (Jun 24, 2022)
4-188003648-G-A		not specified	Uncertain significance (Jan 16, 2024)
4-188003662-G-T		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFP42	protein_coding	protein_coding	ENST00000326866	1	9280

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.448	194	177	1.09	0.0000106	2022
Missense in Polyphen		43	51.924	0.82813		557
Synonymous	0.263	71	73.9	0.961	0.00000512	599
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the reprogramming of X-chromosome inactivation during the acquisition of pluripotency. Required for efficient elongation of TSIX, a non-coding RNA antisense to XIST. Binds DXPas34 enhancer within the TSIX promoter. Involved in ES cell self-renewal (By similarity). {ECO:0000250}.
• Pathway: Cardiac Progenitor Differentiation;Preimplantation Embryo (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.465
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.76

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.265

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp42
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;male gonad development;female gonad development;meiotic cell cycle
• Cellular component: nuclear chromatin;nucleus;transcription factor complex;cytoplasm;PcG protein complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;sequence-specific DNA binding;metal ion binding