ZHX1

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

Basic information

Region (hg38): 8:123248451-123275541

Links

ENSG00000165156 ∙ NCBI:11244 ∙ OMIM:604764 ∙ HGNC:12871 ∙ Uniprot:Q9UKY1 ∙ 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 ZHX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZHX1 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						0
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in ZHX1

This is a list of pathogenic ClinVar variants found in the ZHX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-123253351-G-A		not specified	Uncertain significance (Jul 12, 2023)
8-123253569-T-C		not specified	Uncertain significance (May 10, 2024)
8-123253665-C-G		not specified	Uncertain significance (Apr 25, 2023)
8-123253678-G-A		not specified	Uncertain significance (May 26, 2024)
8-123253696-G-A		not specified	Uncertain significance (Feb 15, 2023)
8-123253710-C-T		not specified	Uncertain significance (Dec 14, 2023)
8-123253980-G-C		not specified	Uncertain significance (May 23, 2023)
8-123253984-C-A		not specified	Uncertain significance (Nov 13, 2023)
8-123253995-T-C		not specified	Uncertain significance (Oct 02, 2023)
8-123254172-A-G		not specified	Uncertain significance (Mar 02, 2023)
8-123254182-T-A		not specified	Uncertain significance (Dec 13, 2023)
8-123254313-T-C		not specified	Uncertain significance (May 08, 2024)
8-123254436-G-A		not specified	Uncertain significance (Jan 17, 2024)
8-123254454-A-G		not specified	Uncertain significance (Feb 17, 2023)
8-123254472-G-A		not specified	Uncertain significance (Oct 10, 2023)
8-123254478-T-C		not specified	Uncertain significance (May 13, 2024)
8-123254595-T-C		not specified	Uncertain significance (Mar 25, 2024)
8-123254622-G-A		not specified	Uncertain significance (Feb 26, 2024)
8-123254638-T-C		not specified	Uncertain significance (Aug 30, 2021)
8-123254647-C-T		not specified	Uncertain significance (Jul 13, 2021)
8-123254807-A-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
8-123254992-C-T		not specified	Uncertain significance (May 30, 2024)
8-123255016-T-C		not specified	Uncertain significance (Jun 30, 2022)
8-123255096-T-C		not specified	Uncertain significance (Jun 22, 2021)
8-123255112-C-T		not specified	Uncertain significance (May 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZHX1	protein_coding	protein_coding	ENST00000395571	1	27086

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.804	0.196	125728	0	7	125735	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	339	457	0.742	0.0000232	5775
Missense in Polyphen		61	150.55	0.40519		1916
Synonymous	0.431	152	159	0.957	0.00000805	1681
Loss of Function	3.96	5	27.4	0.183	0.00000135	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000353	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor. Increases DNMT3B- mediated repressive transcriptional activity when DNMT3B is tethered to DNA. May link molecule between DNMT3B and other co- repressor proteins. {ECO:0000269|PubMed:12237128}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.254
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.46

Haploinsufficiency Scores

• pHI: 0.311
• hipred: Y
• hipred_score: 0.783
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zhx1

Gene ontology

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