ZHX3

zinc fingers and homeoboxes 3, the group of ZF class homeoboxes and pseudogenes|Zinc fingers C2H2-type

Basic information

Region (hg38): 20:41178447-41317731

Previous symbols: [ "TIX1" ]

Links

ENSG00000174306 ∙ NCBI:23051 ∙ OMIM:609598 ∙ HGNC:15935 ∙ Uniprot:Q9H4I2 ∙ 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 ZHX3 gene.

• not provided (64 variants)
• Inborn genetic diseases (39 variants)
• Coronary artery atherosclerosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZHX3 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				18	6	24
missense			59	4	6	69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	59	23	13

Variants in ZHX3

This is a list of pathogenic ClinVar variants found in the ZHX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-41185089-G-A			Benign (May 19, 2021)
20-41185209-G-A			Likely benign (Jul 15, 2023)
20-41185212-A-G			Uncertain significance (Feb 16, 2023)
20-41185218-T-C			Likely benign (Sep 03, 2023)
20-41185409-A-AG			Benign (May 19, 2021)
20-41202041-C-G			Likely benign (Jul 03, 2022)
20-41202065-C-T		not specified	Uncertain significance (Aug 09, 2021)
20-41202080-C-A		not specified	Uncertain significance (Jan 23, 2024)
20-41202082-C-T			Likely benign (Sep 21, 2023)
20-41202083-G-C		not specified	Uncertain significance (Dec 20, 2023)
20-41202147-A-T			Uncertain significance (Apr 20, 2023)
20-41202162-T-C			Uncertain significance (Sep 01, 2022)
20-41202228-T-G		not specified	Uncertain significance (Dec 20, 2023)
20-41202256-C-T		not specified	Uncertain significance (Jan 26, 2022)
20-41202259-T-C		ZHX3-related disorder	Benign (Jan 26, 2024)
20-41202289-G-A			Likely benign (Jan 29, 2024)
20-41202359-T-C			Uncertain significance (Jun 24, 2023)
20-41202378-G-A		not specified	Uncertain significance (Jul 07, 2022)
20-41202380-T-A		not specified	Uncertain significance (Jul 12, 2022)
20-41202381-T-A		not specified	Uncertain significance (Oct 16, 2023)
20-41202391-A-G			Likely benign (Apr 16, 2021)
20-41202394-G-A			Likely benign (May 10, 2022)
20-41202411-G-C			Uncertain significance (Jan 04, 2023)
20-41202416-T-C		not specified	Uncertain significance (Jan 04, 2024)
20-41202422-C-T			Uncertain significance (Apr 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZHX3	protein_coding	protein_coding	ENST00000309060	2	139225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0508	0.949	125733	0	13	125746	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	439	534	0.823	0.0000296	6293
Missense in Polyphen		113	185.74	0.60838		2220
Synonymous	0.168	213	216	0.985	0.0000126	1938
Loss of Function	3.61	8	29.0	0.276	0.00000164	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000142	0.000139
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000721	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor. Involved in the early stages of mesenchymal stem cell (MSC) osteogenic differentiation. Is a regulator of podocyte gene expression during primary glomerula disease. Binds to promoter DNA. {ECO:0000269|PubMed:12659632, ECO:0000269|PubMed:21174497}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.291
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.21

Haploinsufficiency Scores

• pHI: 0.164
• hipred: Y
• hipred_score: 0.670
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.875

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zhx3
• Phenotype: growth/size/body region phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;cell differentiation;positive regulation of osteoblast differentiation;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;protein homodimerization activity;metal ion binding;protein heterodimerization activity