ZNF142

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the Kruppel family of C2H2-type zinc finger proteins. It contains 31 C2H2-type zinc fingers and may be involved in transcriptional regulation. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2013]

MANE transcript

NM_001379659.1

Inheritance

ClinVar variants

P:55U:313B:99

Top phenotype

Neurodevelopmental disorder with impaired speech and hyperkinetic movements

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr2:218,633,329-218,659,655

External References & Databases

Ensembl (ENSG00000115568)

Transcript & Mutation Effects

hg38 • Region Span ~26.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorder with impaired speech and hyperkinetic movementsMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0032741

Submitter: Ambry Genetics

neurodevelopmental disorder with impaired speech and hyperkinetic movementsSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032741

Submitter: G2P

neurodevelopmental disorder with impaired speech and hyperkinetic movementsSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032741

Submitter: PanelApp Australia

neurodevelopmental disorder with impaired speech and hyperkinetic movementsSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032741

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Neurodevelopmental disorder with impaired speech and hyperkinetic movementsAR

Manifestation: Neurologic

Intervention: General

Rationale: 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

Refs: 31036918

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF142 variants in ClinVar

7 Conditions Cataloged

Inborn genetic diseasesTotal: 284

not providedTotal: 139

Neurodevelopmental disorder with impaired speech and hyperkinetic movementsTotal: 79

ZNF142-related disorderTotal: 36

not specifiedTotal: 25

SeizureTotal: 1

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001379659.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	50 clinvar	4 clinvar	56
missense		4 clinvar	307 clinvar	42 clinvar	3 clinvar	356
nonsense	7 clinvar	11 clinvar	1 clinvar			19
start loss						0
frameshift	13 clinvar	16 clinvar	2 clinvar			31
splice donor/acceptor (+/-2bp)	2 clinvar	2 clinvar	1 clinvar			5
Total	22	33	313	92	7	467

Highest pathogenic variant AF is 0.00039938258

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001379659.1	RefSeq	NP_001366588.1	8	MANE Select
ENST00000411696.7	Ensembl	ENSP00000398798.3	8	MANE Select
NM_001105537.4	RefSeq	NP_001099007.1	7	Standard
NM_001366287.2	RefSeq	NP_001353216.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
biological_process

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
molecular_function
DNA binding
metal ion binding

Cellular Component

cellular_component
nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000411696
Coding exons: 7
Length: 21740
Individuals with no LoFs: 125029
Homozygous LoFs: 0
Heterozygous LoFs: 115
Defined: 125144
p: 0.000460

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.241	962	983	0.978	0.0000607	10999
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00073	0.00072	rare
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.00055	0.00054	rare
South Asian	0.00061	0.00059	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.796

Gene Damage Prediction

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