ZHX2

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

Basic information

Region (hg38): 8:122781655-122974510

Links

ENSG00000178764 ∙ NCBI:22882 ∙ OMIM:609185 ∙ HGNC:18513 ∙ Uniprot:Q9Y6X8 ∙ 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 ZHX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZHX2 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	4	6
missense			51	4	1	56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	6	5

Variants in ZHX2

This is a list of pathogenic ClinVar variants found in the ZHX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-122951540-A-G			Likely benign (Jun 01, 2022)
8-122951616-G-A		not specified	Likely benign (Jun 03, 2022)
8-122951661-C-T		not specified	Uncertain significance (Sep 17, 2021)
8-122951826-C-A		not specified	Uncertain significance (Jan 24, 2023)
8-122951840-C-T			Benign (Aug 16, 2018)
8-122951841-G-A		not specified	Uncertain significance (Jul 14, 2021)
8-122951847-G-T		not specified	Uncertain significance (Jun 24, 2022)
8-122951869-A-C		not specified	Uncertain significance (Dec 14, 2023)
8-122951881-C-T		not specified	Uncertain significance (Dec 06, 2022)
8-122951936-G-T		not specified	Uncertain significance (May 26, 2022)
8-122951946-C-T		not specified	Uncertain significance (May 31, 2024)
8-122951979-G-A		not specified	Uncertain significance (May 06, 2024)
8-122952144-G-A			Benign (Jul 13, 2018)
8-122952147-G-A		not specified	Uncertain significance (Jun 18, 2024)
8-122952154-C-A		not specified	Uncertain significance (Sep 16, 2021)
8-122952160-G-A		not specified	Uncertain significance (Jul 12, 2022)
8-122952199-G-A		not specified	Uncertain significance (Jul 14, 2023)
8-122952213-C-T		not specified	Uncertain significance (May 26, 2023)
8-122952214-T-A		not specified	Uncertain significance (Jan 23, 2024)
8-122952238-T-G		not specified	Uncertain significance (Jan 16, 2024)
8-122952403-C-T		not specified	Uncertain significance (Jan 31, 2024)
8-122952515-C-T			Benign (Jul 02, 2018)
8-122952558-G-A		not specified	Uncertain significance (Feb 07, 2023)
8-122952573-A-G		not specified	Uncertain significance (Sep 17, 2021)
8-122952583-C-T		not specified	Uncertain significance (Mar 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZHX2	protein_coding	protein_coding	ENST00000314393	1	193118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0337	0.966	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.759	452	500	0.904	0.0000316	5479
Missense in Polyphen		121	183.4	0.65976		2126
Synonymous	-1.51	244	216	1.13	0.0000160	1697
Loss of Function	3.49	8	27.9	0.287	0.00000155	309

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor. Represses the promoter activity of the CDC25C gene stimulated by NFYA. {ECO:0000269|PubMed:12741956}.

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.0883
• rvis_EVS: -1.1
• rvis_percentile_EVS: 6.95

Haploinsufficiency Scores

• pHI: 0.335
• hipred: Y
• hipred_score: 0.749
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zhx2
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;mRNA catabolic process;somatic stem cell population maintenance;negative regulation of neuron differentiation;negative regulation of transcription, DNA-templated;retinal bipolar neuron differentiation
• Cellular component: nucleus;nucleoplasm;cytosol;plasma membrane
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;identical protein binding;protein homodimerization activity;metal ion binding;protein heterodimerization activity