GeneBe

TSHZ3

teashirt zinc finger homeobox 3, the group of Zinc fingers C2H2-type|ZF class homeoboxes and pseudogenes

Basic information

Region (hg38): 19:31149979-31349436

Previous symbols: [ "ZNF537" ]

Links

ENSG00000121297 ∙ NCBI:57616 ∙ OMIM:614119 ∙ HGNC:30700 ∙ Uniprot:Q63HK5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • congenital anomaly of kidney and urinary tract (Limited), mode of inheritance: AD
  • autism spectrum disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSHZ3 gene.

  • not_specified (134 variants)
  • TSHZ3-related_disorder (30 variants)
  • not_provided (8 variants)
  • Congenital_anomaly_of_kidney_and_urinary_tract (5 variants)
  • Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSHZ3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020856.4. 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
20
clinvar
1
clinvar
 21
missense
2
clinvar
134
clinvar
8
clinvar
1
clinvar
 145
nonsense
1
clinvar
 1
start loss
1
 1
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 2 136 28 2

Highest pathogenic variant AF is 0.0008733874

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TSHZ3protein_codingprotein_codingENST00000240587 274603
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9910.00947125744041257480.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.835196510.7980.00004087131
Missense in Polyphen165266.960.618063070
Synonymous-0.9683202991.070.00002242142
Loss of Function4.30327.20.1100.00000132371

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006190.0000615
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001770.0000176
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Transcriptional regulator involved in developmental processes. Function in association with APBB1, SET and HDAC factors as a transcriptional repressor, that inhibits the expression of CASP4. TSHZ3-mediated transcription repression involves the recruitment of histone deacetylases HDAC1 and HDAC2. Associates with chromatin in a region surrounding the CASP4 transcriptional start site(s) (PubMed:19343227). Regulates the development of neurons involved in both respiratory rhythm and airflow control. Promotes maintenance of nucleus ambiguus (nA) motoneurons, which govern upper airway function, and establishes a respiratory rhythm generator (RRG) activity compatible with survival at birth. Involved in the differentiation of the proximal uretic smooth muscle cells during developmental processes. Involved in the up-regulation of myocardin, that directs the expression of smooth muscle cells in the proximal ureter (By similarity). Involved in the modulation of glutamatergic synaptic transmission and long-term synaptic potentiation (By similarity). {ECO:0000250|UniProtKB:Q8CGV9, ECO:0000269|PubMed:19343227}.;
Disease
DISEASE: Note=TSHZ3 haploinsufficiency due to proximal chromosome 19q13.11 deletions causes a neurodevelopmental disorder characterized by developmental delay, absent or delayed speech, intellectual disability, and autistic features. Some patients may have reanal tract abnormalities. {ECO:0000269|PubMed:27668656}.;

Recessive Scores

pRec
0.122

Intolerance Scores

loftool
0.135
rvis_EVS
-1.72
rvis_percentile_EVS
2.49

Haploinsufficiency Scores

pHI
0.866
hipred
Y
hipred_score
0.728
ghis
0.574

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.762

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tshz3
Phenotype
integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; renal/urinary system phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;regulation of respiratory gaseous exchange by neurological system process;regulation of transcription by RNA polymerase II;multicellular organism development;negative regulation of transcription, DNA-templated;positive regulation of synaptic transmission, glutamatergic;long-term synaptic potentiation
Cellular component
nucleus;nucleoplasm;growth cone
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;chromatin binding;protein binding;metal ion binding