ZNF142

zinc finger protein 142, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 2:218633329-218659655

Links

ENSG00000115568

∙ NCBI:7701 ∙ OMIM:604083 ∙ HGNC:12927 ∙ Uniprot:P52746 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

neurodevelopmental disorder with impaired speech and hyperkinetic movements (Strong), mode of inheritance: AR
neurodevelopmental disorder with impaired speech and hyperkinetic movements (Moderate), mode of inheritance: AR
neurodevelopmental disorder with impaired speech and hyperkinetic movements (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with impaired speech and hyperkinetic movements	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	31036918

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF142 gene.

Inborn_genetic_diseases (242 variants)
not_provided (102 variants)
Neurodevelopmental_disorder_with_impaired_speech_and_hyperkinetic_movements (71 variants)
ZNF142-related_disorder (27 variants)
not_specified (6 variants)
Seizure (1 variants)
Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF142 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001379659.1. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	29 clinvar	3 clinvar	33
missense	1 clinvar	4 clinvar	259 clinvar	36 clinvar	3 clinvar	303
nonsense	8 clinvar	6 clinvar	2 clinvar			16
start loss						0
frameshift	10 clinvar	10 clinvar	2 clinvar			22
splice donor/acceptor (+/-2bp)	2 clinvar	2 clinvar				4
Total	21	22	264	65	6

Highest pathogenic variant AF is 0.00004213433

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF142	protein_coding	protein_coding	ENST00000411696	7	21740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.81e-16	0.995	125029	0	115	125144	0.000460

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.241	962	983	0.978	0.0000607	10999
Missense in Polyphen		68	66.127	1.0283		710
Synonymous	0.509	361	374	0.966	0.0000195	3451
Loss of Function	2.84	34	57.2	0.595	0.00000361	660

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000416
Ashkenazi Jewish	0.000105	0.0000993
East Asian	0.000725	0.000722
Finnish	0.000325	0.000325
European (Non-Finnish)	0.000546	0.000538
Middle Eastern	0.000725	0.000722
South Asian	0.000612	0.000588
Other	0.000494	0.000492

dbNSFP

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.0977

Intolerance Scores

loftool: 0.903
rvis_EVS: -0.65
rvis_percentile_EVS: 16.45

Haploinsufficiency Scores

pHI: 0.162
hipred: N
hipred_score: 0.251
ghis: 0.550

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.796

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Zfp142
Phenotype: hematopoietic system phenotype; hearing/vestibular/ear phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;biological_process
Cellular component: cellular_component;nucleus
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA binding;metal ion binding