ZNF142
Basic information
Region (hg38): 2:218633329-218659655
Links
Phenotypes
GenCC
Source:
- 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:
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
- 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 | 27 | ||||
missense | 133 | 14 | 155 | |||
nonsense | 9 | |||||
start loss | 0 | |||||
frameshift | 13 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 1 | ||||
non coding | 14 | 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) | ||
2-218633716-T-C | not specified | Uncertain significance (Apr 19, 2024) | ||
2-218633744-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
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) | ||
2-218636483-T-G | not specified | Uncertain significance (May 13, 2024) | ||
2-218636557-C-G | not specified | Uncertain significance (Mar 19, 2024) | ||
2-218636564-G-C | not specified | Uncertain significance (Apr 16, 2024) | ||
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) |
GnomAD
Source:
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:
- 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