TSHZ1
protein-codingteashirt 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]
- SDCCAG33
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~79.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0011921
Submitter: PanelApp Australia
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).
Inheritance Pattern: AD
Disease ID:MONDO:0011921
Submitter: Labcorp Genetics (formerly Invitae)
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.
Inheritance Pattern: AD
Disease ID:MONDO:0011921
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0011921
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0008652
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TSHZ1 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 51 | 3 | 54 | |||
| missense | 203 | 34 | 5 | 242 | ||
| nonsense | 1 | 1 | ||||
| start loss | 2 | 2 | ||||
| frameshift | 1 | 5 | 1 | 7 | ||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 211 | 86 | 8 | 306 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001295139.1 | 2 | MANE Select | |
| Ensembl | ENSP00000464391.1 | 2 | MANE Select | |
| RefSeq | NP_005777.3 | 1 | Standard | |
| Ensembl | ENSP00000323584.5 | 1 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.29 | 553 | 645 | 0.857 | 0.0000410 | 6767 |
| Missense (PolyPhen) | 203 | 293.64 | 0.69133 | 3160 | ||
| Synonymous | -1.27 | 342 | 313 | 1.09 | 0.0000243 | 2071 |
| Loss of Function | 4.38 | 2 | 26.2 | 0.0764 | 0.00000119 | 348 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000059 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |