ZNF142

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

Basic information

Region (hg38): 2:218633328-218659655

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 (102 variants)
• not provided (63 variants)
• Neurodevelopmental disorder with impaired speech and hyperkinetic movements (35 variants)
• not specified (4 variants)
• - (2 variants)
• Global developmental delay (1 variants)
• Intellectual disability;Seizure (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.

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				14	5	19
missense			109	9	5	123
nonsense	4	4	2			10
start loss						0
frameshift	4	6	3			13
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region				1		1
non coding			12	2	8	22
Total	8	11	127	25	18

Highest pathogenic variant AF is 0.0000131

Variants in ZNF142

This is a list of pathogenic ClinVar variants found in the ZNF142 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-218633716-T-C		not specified	Uncertain significance (Apr 08, 2022)
2-218634143-C-T		not specified	Uncertain significance (Dec 14, 2022)
2-218634144-G-A		not specified	Uncertain significance (Sep 29, 2022)
2-218634220-G-A		not specified	Uncertain significance (Oct 22, 2021)
2-218634514-C-T		not specified	Uncertain significance (Apr 13, 2022)
2-218634526-G-A		not specified	Uncertain significance (Sep 22, 2022)
2-218635824-T-C		not specified	Uncertain significance (Feb 10, 2022)
2-218635887-G-A		not specified	Uncertain significance (Jun 27, 2022)
2-218635906-G-A			Likely benign (Mar 01, 2022)
2-218635928-A-G		not specified	Uncertain significance (Dec 21, 2022)
2-218636273-G-A		not specified	Uncertain significance (Feb 05, 2024)
2-218636329-G-A		not specified	Likely benign (Sep 17, 2021)
2-218636342-G-A		not specified	Uncertain significance (Aug 08, 2023)
2-218636366-C-T		not specified	Uncertain significance (May 17, 2023)
2-218636384-T-C		not specified	Uncertain significance (Jul 05, 2023)
2-218636477-G-A		not specified	Uncertain significance (Jan 07, 2022)
2-218638365-C-T		Inborn genetic diseases	Likely benign (Feb 22, 2023)
2-218638390-C-T		ZNF142-related disorder	Benign (May 05, 2021)
2-218638409-A-G		Inborn genetic diseases	Uncertain significance (Jun 28, 2023)
2-218638485-C-T		Inborn genetic diseases	Likely benign (Jul 12, 2022)
2-218638535-CA-C			Uncertain significance (Sep 01, 2022)
2-218638555-G-A			Likely benign (Jul 01, 2023)
2-218638556-G-A		Inborn genetic diseases	Uncertain significance (Jul 12, 2022)
2-218638595-C-A		Inborn genetic diseases	Uncertain significance (Sep 12, 2023)
2-218638604-C-T		Inborn genetic diseases	Uncertain significance (Mar 24, 2023)

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
• 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