TSHZ2

teashirt zinc finger homeobox 2, the group of Zinc fingers C2H2-type|ZF class homeoboxes and pseudogenes

Basic information

Region (hg38): 20:52972357-53495330

Previous symbols: [ "C20orf17", "ZNF218" ]

Links

ENSG00000182463 ∙ NCBI:128553 ∙ OMIM:614118 ∙ HGNC:13010 ∙ Uniprot:Q9NRE2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSHZ2 gene.

• Inborn genetic diseases (50 variants)
• Anophthalmia-microphthalmia syndrome (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSHZ2 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				1		1
missense			50	2		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	3	0

Variants in TSHZ2

This is a list of pathogenic ClinVar variants found in the TSHZ2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-53253567-G-A		not specified	Uncertain significance (Sep 26, 2022)
20-53253609-G-A		not specified	Uncertain significance (Feb 02, 2024)
20-53253609-G-C		not specified	Uncertain significance (Oct 10, 2023)
20-53253616-A-C		not specified	Uncertain significance (Nov 08, 2022)
20-53253630-C-T		not specified	Uncertain significance (Jan 10, 2022)
20-53253634-A-G		not specified	Uncertain significance (Apr 24, 2023)
20-53253659-G-C		not specified	Uncertain significance (Dec 20, 2023)
20-53253705-T-G		Anophthalmia-microphthalmia syndrome	Likely benign (Jan 01, 2013)
20-53253740-C-G		not specified	Uncertain significance (Aug 29, 2022)
20-53253756-G-A		not specified	Uncertain significance (Mar 01, 2023)
20-53253762-G-C		not specified	Uncertain significance (Jan 26, 2022)
20-53253763-A-G		not specified	Uncertain significance (Sep 01, 2021)
20-53253817-A-G		not specified	Uncertain significance (Dec 21, 2023)
20-53253840-G-C		not specified	Uncertain significance (Jan 04, 2024)
20-53253969-G-C		not specified	Uncertain significance (Jan 23, 2023)
20-53253995-G-C		not specified	Uncertain significance (Jun 26, 2023)
20-53254009-G-A		not specified	Uncertain significance (Mar 04, 2024)
20-53254026-A-G		not specified	Uncertain significance (Jan 26, 2023)
20-53254120-G-C		not specified	Uncertain significance (Mar 20, 2023)
20-53254123-C-T		not specified	Uncertain significance (Oct 12, 2021)
20-53254177-A-G		not specified	Uncertain significance (Jun 12, 2023)
20-53254192-G-A		not specified	Uncertain significance (Mar 07, 2024)
20-53254216-C-T		not specified	Uncertain significance (Apr 25, 2022)
20-53254302-G-A		not specified	Uncertain significance (Jul 08, 2021)
20-53254306-C-T		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSHZ2	protein_coding	protein_coding	ENST00000371497	2	522924

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.981	0.0186	125739	0	8	125747	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.602	556	597	0.931	0.0000344	6850
Missense in Polyphen		234	292.96	0.79874		3402
Synonymous	-0.119	259	257	1.01	0.0000174	1986
Loss of Function	4.63	5	34.2	0.146	0.00000180	422

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000109	0.000109
South Asian	0.0000683	0.0000653
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: 0.118

Intolerance Scores

• loftool: 0.135
• rvis_EVS: -0.92
• rvis_percentile_EVS: 9.83

Haploinsufficiency Scores

• pHI: 0.136
• hipred: Y
• hipred_score: 0.543
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.755

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tshz2
• 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); embryo phenotype

Zebrafish Information Network

• Gene name: tshz2
• Affected structure: ceratobranchial cartilage
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;multicellular organism development
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;chromatin binding;protein binding;metal ion binding