TSHZ1

protein-coding

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

Gene summary

This gene encodes a colon cancer antigen that was defined by serological analysis of recombinant cDNA expression libraries. The encoded protein is a member of the teashirt C2H2-type zinc-finger protein family and may be involved in transcriptional regulation of developmental processes. Mutations in this gene may be associated with congenital aural atresia syndrome. [provided by RefSeq, Jan 2012]

Previous symbols:
  • SDCCAG33

MANE transcript

NM_001308210.2

Inheritance

AD

ClinVar variants

P:1U:211B:94

Top phenotype

Aural atresia, congenital

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr18:75,210,755-75,289,950

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~79.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

aural atresia, congenitalSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011921

Submitter: PanelApp Australia

aural atresia, congenitalLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0011921

Submitter: ClinGen

The TSHZ1 gene was first reported in relation to autosomal dominant congenital aural atresia/deafness in 2011 (Feenstra et al., PMID 22152683). 7 variants (missense, nonsense, frameshift) that have been reported in at least 11 probands in 3 publications (PMIDs: 22152683, 35487415, 36597107) are included in this curation. The mechanism of pathogenicity appears to be loss-of-function. This gene-disease relationship is also supported by experimental evidence (mouse models, expression-level evidence; PMIDs: 17586487, 24487590). Temporal and spatial expression of TSHZ1 mRNA during development of the middle ear is consistent with the phenotype (PMID: 17586487). The homozygous TSHZ1 null mouse model showed a middle ear malformation, as well as neonatal lethality. A conditional nervous system-specific TSHZ1 knock out mouse model demonstrated hyposmia (PMIDs: 17586487, 24487590). In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This GDR was originally evaluated by the Syndromic Disorders GCEP on June 19, 2020. It was reevaluated on July 23, 2024. A new phenotype, congenital vertical talus, was reported in probands, in addition to more cases of deafness (PMIDs: 35487415, 36597107). An additional two missense variants were added to the curation from two probands in one publication (PMID: 36597107). Despite new genetic evidence, as a result of this reevaluation, the classification did not change (SOP Version 10).

aural atresia, congenitalLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0011921

Submitter: Labcorp Genetics (formerly Invitae)

aural atresia, congenitalLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0011921

Submitter: Illumina

The TSHZ1 gene is located on chromosome 18 at 18q22.3 and encodes the teashirt zinc finger homeobox 1 protein. TSHZ1 is a putative zinc finger transcription factor that is expressed throughout the embryo during development (15834955: Caubit et al. 2005; 17586487: Core et al. 2007). TSHZ1 was first reported in relation to autosomal dominant congenital aural atresia in 2011 (22152683: Feenstra et al. 2011). Evidence supporting this gene-disease relationship includes case level data and experimental data. At least two variants, a stop gained variant and a frameshift variant, have been found in a heterozygous state in two individuals from one report in the literature, both with a phenotype of congenital aural atresia and hyposmia (22152683: Feenstra et al. 2011; 24487590: Ragancokova et al. 2014). Temporal and spatial expression of Tshz1 mRNA during development of the middle ear is consistent with the phenotype (17586487: Core et al. 2007). Embryos of the homozygous Tsh2 null mouse model showed a middle ear malformation as well as neonatal lethality, and a conditional nervous system-specific Tshz1 knock out mouse model demonstrated hyposmia (17586487: Core et al. 2007; 24487590: Ragancokova et al. 2014). In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship.

aural atresia, congenitalLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0011921

Submitter: G2P

aural atresia, congenitalLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0011921

Submitter: Ambry Genetics

congenital vertical talusLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0008652

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Aural atresia, congenitalAD

Manifestation: Audiologic/Otolaryngologic; Craniofacial

Intervention: Audiologic/Otolaryngologic

Rationale: Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development

Comments: The condition may be recognizable from physical examination

Refs: 22152683; 24487590Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TSHZ1 variants in ClinVar

5 Conditions Cataloged
not specifiedTotal: 239
TSHZ1-related disorderTotal: 90
not providedTotal: 21
Aural atresia, congenitalTotal: 15
EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001308210.2. 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.

EffectPLPVUSLBBSum
synonymous
51
clinvar
3
clinvar
54
missense
203
clinvar
34
clinvar
5
clinvar
242
nonsense
1
clinvar
1
start loss
2
clinvar
2
frameshift
1
clinvar
5
clinvar
1
clinvar
7
splice donor/acceptor (+/-2bp)
0
Total01211868306
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001308210.2RefSeqNP_001295139.12MANE Select
ENST00000580243.3EnsemblENSP00000464391.12MANE Select
NM_005786.6RefSeqNP_005777.31Standard
ENST00000322038.5EnsemblENSP00000323584.51Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

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

Cellular Component

  • nucleus

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000322038
Coding exons
1
Length
79196
Individuals with no LoFs
125741
Homozygous LoFs
0
Heterozygous LoFs
6
Defined
125747
p
0.0000239
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.295536450.8570.00004106767
Missense (PolyPhen)203293.640.691333160
Synonymous-1.273423131.090.00002432071
Loss of Function4.38226.20.07640.00000119348

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000590.000058rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.0000180.000018rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.737

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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