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

ENSG00000179981 ∙ NCBI:10194 ∙ OMIM:614427 ∙ HGNC:10669 ∙ Uniprot:Q6ZSZ6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Aural atresia, congenital	AD	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Craniofacial	22152683; 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	5	7
missense			55	2	2	59
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15	1		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)
18-75210894-TGA-T		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75210894-TGAG-T		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75210894-T-TG		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75210894-T-TGA		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75210894-T-TGG		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75210895-GA-G		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75210896-A-AG		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75210896-A-AGG		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75211003-A-AG		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75211003-A-AGG		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75211133-G-GC		Aural atresia, congenital	Likely benign (Jun 14, 2016)
18-75211150-G-A		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75211151-C-G		Aural atresia, congenital	Uncertain significance (Jun 14, 2016)
18-75211879-G-A		Aural atresia, congenital	Uncertain significance (Feb 13, 2019)
18-75285534-A-G		TSHZ1-related disorder	Benign (Jul 15, 2019)
18-75285570-G-A		not specified	Uncertain significance (Feb 03, 2022)
18-75285574-C-T		not specified	Uncertain significance (Oct 14, 2021)
18-75285575-G-A			Likely benign (Feb 01, 2023)
18-75285607-C-T		not specified	Uncertain significance (May 18, 2022)
18-75285634-C-T		TSHZ1-related disorder	Uncertain significance (Sep 28, 2022)
18-75285636-C-A		not specified	Uncertain significance (May 26, 2022)
18-75285683-C-T		TSHZ1-related disorder	Likely benign (Feb 01, 2023)
18-75285722-C-T		TSHZ1-related disorder	Benign (Mar 15, 2023)
18-75285727-C-T		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSHZ1	protein_coding	protein_coding	ENST00000322038	1	79196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00270	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	553	645	0.857	0.0000410	6767
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000592	0.0000592
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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