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GeneBe

TSHZ1

teashirt zinc finger homeobox 1, the group of Zinc fingers C2H2-type|ZF class homeoboxes and pseudogenes

Basic information

Region (hg38): 18:75210754-75289950

Previous symbols: [ "SDCCAG33" ]

Links

ENSG00000179981NCBI:10194OMIM:614427HGNC:10669Uniprot:Q6ZSZ6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • aural atresia, congenital (Limited), mode of inheritance: AD
  • aural atresia, congenital (Limited), mode of inheritance: AD
  • aural atresia, congenital (Limited), mode of inheritance: AD
  • aural atresia, congenital (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Aural atresia, congenitalADAudiologic/OtolaryngologicEarly recognition and treatment of hearing impairment may improve outcomes, including speech and language developmentAudiologic/Otolaryngologic; Craniofacial22152683; 24487590
The condition may be recognizable from physical examination

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSHZ1 gene.

  • Inborn genetic diseases (51 variants)
  • Aural atresia, congenital (24 variants)
  • not provided (8 variants)
  • not specified (4 variants)
  • TSHZ1-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSHZ1 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
2
clinvar
5
clinvar
7
missense
55
clinvar
2
clinvar
2
clinvar
59
nonsense
0
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
15
clinvar
1
clinvar
16
Total 0 0 71 5 7

Variants in TSHZ1

This is a list of pathogenic ClinVar variants found in the TSHZ1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
18-75210891-G-GT Aural atresia, congenital Uncertain significance (Jun 14, 2016)327764
18-75210894-TGA-T Aural atresia, congenital Uncertain significance (Jun 14, 2016)327768
18-75210894-TGAG-T Aural atresia, congenital Uncertain significance (Jun 14, 2016)327769
18-75210894-T-TG Aural atresia, congenital Uncertain significance (Jun 14, 2016)327765
18-75210894-T-TGA Aural atresia, congenital Uncertain significance (Jun 14, 2016)327766
18-75210894-T-TGG Aural atresia, congenital Uncertain significance (Jun 14, 2016)327767
18-75210895-GA-G Aural atresia, congenital Uncertain significance (Jun 14, 2016)327770
18-75210896-A-AG Aural atresia, congenital Uncertain significance (Jun 14, 2016)327771
18-75210896-A-AGG Aural atresia, congenital Uncertain significance (Jun 14, 2016)327772
18-75211003-A-AG Aural atresia, congenital Uncertain significance (Jun 14, 2016)327778
18-75211003-A-AGG Aural atresia, congenital Uncertain significance (Jun 14, 2016)327779
18-75211133-G-GC Aural atresia, congenital Likely benign (Jun 14, 2016)327785
18-75211150-G-A Aural atresia, congenital Uncertain significance (Jun 14, 2016)327786
18-75211151-C-G Aural atresia, congenital Uncertain significance (Jun 14, 2016)327787
18-75211879-G-A Aural atresia, congenital Uncertain significance (Feb 13, 2019)3062035
18-75285534-A-G TSHZ1-related condition Benign (Jul 15, 2019)3043118
18-75285570-G-A not specified Uncertain significance (Feb 03, 2022)3183682
18-75285574-C-T not specified Uncertain significance (Oct 14, 2021)2255404
18-75285575-G-A Likely benign (Feb 01, 2023)2648811
18-75285607-C-T not specified Uncertain significance (May 18, 2022)2350836
18-75285634-C-T TSHZ1-related condition Uncertain significance (Sep 28, 2022)2628706
18-75285636-C-A not specified Uncertain significance (May 26, 2022)2291308
18-75285683-C-T TSHZ1-related condition Likely benign (Feb 01, 2023)2648812
18-75285722-C-T TSHZ1-related condition Benign (Mar 15, 2023)1260276
18-75285727-C-T not specified Uncertain significance (Dec 27, 2023)3183674

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TSHZ1protein_codingprotein_codingENST00000322038 179196
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9970.00270125741061257470.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.295536450.8570.00004106767
Missense in Polyphen203293.640.691333160
Synonymous-1.273423131.090.00002432071
Loss of Function4.38226.20.07640.00000119348

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005920.0000592
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.0001090.000109
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Probable transcriptional regulator involved in developmental processes. May act as a transcriptional repressor (Potential). {ECO:0000305}.;

Recessive Scores

pRec
0.137

Intolerance Scores

loftool
0.0756
rvis_EVS
-1.29
rvis_percentile_EVS
5.01

Haploinsufficiency Scores

pHI
0.192
hipred
Y
hipred_score
0.728
ghis
0.537

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.737

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tshz1
Phenotype
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; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; craniofacial phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;anterior/posterior pattern specification;middle ear morphogenesis;soft palate development
Cellular component
nucleus
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;chromatin binding;metal ion binding