ZNF442

zinc finger protein 442, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:12345944-12365905

Links

ENSG00000198342 ∙ NCBI:79973 ∙ ∙ HGNC:20877 ∙ Uniprot:Q9H7R0 ∙ 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 ZNF442 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF442 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			53	3		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	3	0

Variants in ZNF442

This is a list of pathogenic ClinVar variants found in the ZNF442 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12349711-T-C		not specified	Uncertain significance (Apr 08, 2024)
19-12349721-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-12349786-T-C		not specified	Uncertain significance (Aug 12, 2021)
19-12349837-C-T		not specified	Uncertain significance (May 27, 2022)
19-12349838-G-A		not specified	Uncertain significance (Apr 22, 2022)
19-12349842-G-T		not specified	Uncertain significance (May 07, 2024)
19-12349852-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-12349856-A-G		not specified	Uncertain significance (Feb 05, 2025)
19-12349883-C-T		not specified	Uncertain significance (Feb 07, 2025)
19-12349900-T-C		not specified	Uncertain significance (Mar 25, 2024)
19-12349939-C-A		not specified	Uncertain significance (Jan 17, 2025)
19-12349970-T-A		not specified	Likely benign (Aug 11, 2022)
19-12350027-T-C		not specified	Uncertain significance (Jul 12, 2022)
19-12350177-T-C		not specified	Uncertain significance (Dec 27, 2023)
19-12350243-G-T		not specified	Uncertain significance (Oct 17, 2023)
19-12350308-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-12350342-T-C		not specified	Likely benign (Jun 28, 2023)
19-12350375-G-A		not specified	Uncertain significance (Dec 13, 2022)
19-12350378-C-T		not specified	Uncertain significance (Apr 06, 2023)
19-12350419-T-C		not specified	Likely benign (Dec 26, 2023)
19-12350423-G-A		not specified	Uncertain significance (Nov 18, 2022)
19-12350458-G-A		not specified	Uncertain significance (Jan 24, 2023)
19-12350492-G-T		not specified	Uncertain significance (Jan 27, 2025)
19-12350498-A-C		not specified	Uncertain significance (Mar 31, 2023)
19-12350552-C-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF442	protein_coding	protein_coding	ENST00000242804	4	16535

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0305	0.822	125655	0	4	125659	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.716	364	328	1.11	0.0000163	4181
Missense in Polyphen		118	126.94	0.92955		1717
Synonymous	-0.765	117	107	1.09	0.00000501	1086
Loss of Function	1.13	3	5.97	0.503	2.53e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000304	0.0000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000902	0.00000880
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

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: 0.950
• rvis_EVS: 2.16
• rvis_percentile_EVS: 98.01

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.112
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp971

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