GeneBe

POGZ

pogo transposable element derived with ZNF domain, the group of Helix-turn-helix CENPB type domain containing|DNA transposon derived genes

Basic information

Region (hg38): 1:151402724-151459494

Links

ENSG00000143442 ∙ NCBI:23126 ∙ OMIM:614787 ∙ HGNC:18801 ∙ Uniprot:Q7Z3K3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome (Strong), mode of inheritance: AD
  • intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome (Definitive), mode of inheritance: AD
  • intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome (Supportive), mode of inheritance: AD
  • intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome (Definitive), mode of inheritance: AD
  • intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
White-Sutton syndromeADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic25533962; 26739615

ClinVar

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

  • not_provided (375 variants)
  • Inborn_genetic_diseases (234 variants)
  • Intellectual_disability-microcephaly-strabismus-behavioral_abnormalities_syndrome (224 variants)
  • Autism_spectrum_disorder (51 variants)
  • POGZ-related_disorder (48 variants)
  • not_specified (19 variants)
  • Intellectual_disability (14 variants)
  • Neurodevelopmental_disorder (5 variants)
  • See_cases (4 variants)
  • intellectual_deficiency (1 variants)
  • Truncal_obesity (1 variants)
  • dysmorphy (1 variants)
  • Myopia (1 variants)
  • Decreased_lacrimation (1 variants)
  • Inability_to_walk_by_childhood/adolescence (1 variants)
  • Microcephaly (1 variants)
  • Wide_mouth (1 variants)
  • Seizure (1 variants)
  • Short_metacarpal (1 variants)
  • Smith-Magenis_Syndrome-like (1 variants)
  • Hypertelorism (1 variants)
  • Obesity (1 variants)
  • Strabismus (1 variants)
  • Generalized_hypotonia (1 variants)
  • Speech_apraxia (1 variants)
  • Global_developmental_delay (1 variants)
  • Hearing_impairment (1 variants)
  • Hypothyroidism (1 variants)
  • Anteverted_nares (1 variants)
  • Severe_global_developmental_delay (1 variants)
  • Hypoplasia_of_the_corpus_callosum (1 variants)
  • Short_stature (1 variants)
  • High_palate (1 variants)
  • Absent_speech (1 variants)
  • Brachycephaly (1 variants)
  • Sensorineural_hearing_loss_disorder (1 variants)
  • Downturned_corners_of_mouth (1 variants)
  • Abnormal_nail_morphology (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POGZ gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015100.4. 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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
75
clinvar
6
clinvar
 86
missense
7
clinvar
12
clinvar
325
clinvar
77
clinvar
2
clinvar
 423
nonsense
30
clinvar
20
clinvar
2
clinvar
 52
start loss
1
 1
frameshift
69
clinvar
43
clinvar
5
clinvar
 117
splice donor/acceptor (+/-2bp)
9
clinvar
7
clinvar
8
clinvar
 24
Total 115 83 345 152 8

Highest pathogenic variant AF is 0.0000069072744

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
POGZprotein_codingprotein_codingENST00000271715 1856742
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.005.95e-9125740051257450.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.515228010.6510.00004479188
Missense in Polyphen203375.170.541094367
Synonymous0.4032943030.9710.00001652910
Loss of Function7.15365.40.04590.00000418650

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001550.000152
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.000008790.00000879
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in mitotic cell cycle progression and is involved in kinetochore assembly and mitotic sister chromatid cohesion. Probably through its association with CBX5 plays a role in mitotic chromosome segregation by regulating aurora kinase B/AURKB activation and AURKB and CBX5 dissociation from chromosome arms. {ECO:0000269|PubMed:20562864}.;
Disease
DISEASE: Note=Defects in POGZ may be associated with neuropsychiatric disorders such as autism spectrum disorders (ASD), bipolar affective disorders and early dementia onset. ASD are characterized by impairments in reciprocal social interaction and communication as well as restricted and stereotyped patterns of interest and activities. ASD include forms with moderate to severe cognitive impairment and milder forms with higher cognitive ability (Asperger syndrome). {ECO:0000269|PubMed:25694107}.; DISEASE: White-Sutton syndrome (WHSUS) [MIM:616364]: A mental retardation syndrome characterized by developmental delay, intellectual disability, hypotonia, behavioral abnormalities, and dysmorphic facial features. Variable features include short stature, microcephaly, strabismus and hearing loss. {ECO:0000269|PubMed:25533962, ECO:0000269|PubMed:26739615}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.108

Intolerance Scores

loftool
0.128
rvis_EVS
-1.53
rvis_percentile_EVS
3.41

Haploinsufficiency Scores

pHI
0.239
hipred
Y
hipred_score
0.775
ghis
0.701

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.985

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Pogz
Phenotype

Zebrafish Information Network

Gene name
pogza
Affected structure
melanocyte
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
regulation of transcription by RNA polymerase II;mitotic sister chromatid cohesion;regulation of gene expression;cell division;kinetochore assembly
Cellular component
nuclear chromatin;nucleus;nucleoplasm;cytoplasm;cytosol;histone methyltransferase complex
Molecular function
RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding