ZNF142

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

Basic information

Region (hg38): 2:218633329-218659655

Links

ENSG00000115568NCBI:7701OMIM:604083HGNC:12927Uniprot:P52746AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodevelopmental disorder with impaired speech and hyperkinetic movementsARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic31036918

ClinVar

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

  • Neurodevelopmental disorder with impaired speech and hyperkinetic movements (5 variants)
  • not provided (2 variants)
  • Inborn genetic diseases (2 variants)
  • Seizure;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.

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
19
clinvar
8
clinvar
27
missense
133
clinvar
14
clinvar
8
clinvar
155
nonsense
4
clinvar
3
clinvar
2
clinvar
9
start loss
0
frameshift
4
clinvar
6
clinvar
3
clinvar
13
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
1
non coding
14
clinvar
2
clinvar
8
clinvar
24
Total 8 10 153 35 24

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
2-218633671-C-T not specified Uncertain significance (Mar 29, 2024)3307340
2-218633716-T-C not specified Uncertain significance (Apr 19, 2024)2374351
2-218633744-G-A not specified Uncertain significance (Jun 10, 2024)3307337
2-218634143-C-T not specified Uncertain significance (Dec 14, 2022)2334900
2-218634144-G-A not specified Uncertain significance (Sep 29, 2022)2383776
2-218634220-G-A not specified Uncertain significance (Oct 22, 2021)2206234
2-218634514-C-T not specified Uncertain significance (Apr 13, 2022)3214458
2-218634526-G-A not specified Uncertain significance (Sep 22, 2022)2226382
2-218635824-T-C not specified Uncertain significance (Feb 10, 2022)2205385
2-218635887-G-A not specified Uncertain significance (Jun 27, 2022)2298004
2-218635906-G-A Likely benign (Mar 01, 2022)2651884
2-218635928-A-G not specified Uncertain significance (Dec 21, 2022)2338933
2-218636273-G-A not specified Uncertain significance (Feb 05, 2024)3214459
2-218636329-G-A not specified Likely benign (Sep 17, 2021)2346245
2-218636342-G-A not specified Uncertain significance (Aug 08, 2023)2617298
2-218636366-C-T not specified Uncertain significance (May 17, 2023)2546906
2-218636384-T-C not specified Uncertain significance (Jul 05, 2023)2609557
2-218636477-G-A not specified Uncertain significance (Jan 07, 2022)2207102
2-218636483-T-G not specified Uncertain significance (May 13, 2024)3307347
2-218636557-C-G not specified Uncertain significance (Mar 19, 2024)3307339
2-218636564-G-C not specified Uncertain significance (Apr 16, 2024)3307344
2-218638365-C-T Inborn genetic diseases Likely benign (Feb 22, 2023)2487790
2-218638390-C-T ZNF142-related disorder Benign (May 05, 2021)1254978
2-218638409-A-G Inborn genetic diseases Uncertain significance (Jun 28, 2023)2606912
2-218638485-C-T Inborn genetic diseases Likely benign (Jul 12, 2022)2273800

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ZNF142protein_codingprotein_codingENST00000411696 721740
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.81e-160.99512502901151251440.000460
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2419629830.9780.000060710999
Missense in Polyphen6866.1271.0283710
Synonymous0.5093613740.9660.00001953451
Loss of Function2.843457.20.5950.00000361660

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004200.000416
Ashkenazi Jewish0.0001050.0000993
East Asian0.0007250.000722
Finnish0.0003250.000325
European (Non-Finnish)0.0005460.000538
Middle Eastern0.0007250.000722
South Asian0.0006120.000588
Other0.0004940.000492

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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