ZNHIT3

zinc finger HIT-type containing 3, the group of Zinc fingers HIT-type

Basic information

Region (hg38): 17:36486629-36499310

Previous symbols: [ "TRIP3" ]

Links

ENSG00000273611 ∙ NCBI:9326 ∙ OMIM:604500 ∙ HGNC:12309 ∙ Uniprot:Q15649 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• PEHO syndrome (Supportive), mode of inheritance: AD
• PEHO syndrome (Moderate), mode of inheritance: AR
• PEHO syndrome (Limited), mode of inheritance: AR
• Mayer-Rokitansky-Kuster-Hauser syndrome (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
PEHO syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dermatologic; Neurologic	28335020

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNHIT3 gene.

• Inborn_genetic_diseases (33 variants)
• not_provided (4 variants)
• PEHO_syndrome (4 variants)
• not_specified (3 variants)
• ZNHIT3-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNHIT3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004773.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense		2	30	3		35
nonsense						0
start loss						0
frameshift			3			3
splice donor/acceptor (+/-2bp)						0
Total	0	2	33	7	0

Highest pathogenic variant AF is 0.0001967253

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Disease: DISEASE: PEHO syndrome (PEHO) [MIM:260565]: An autosomal recessive syndrome characterized by progressive encephalopathy, lack of psychomotor development, severe mental retardation, early onset epileptic seizures, optic nerve/cerebellar atrophy, pedal edema, and early death. {ECO:0000269|PubMed:28335020}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0793

Intolerance Scores

• loftool: 0.503
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.224
• hipred: N
• hipred_score: 0.197

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.843

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Znhit3

Zebrafish Information Network

• Gene name: znhit3
• Affected structure: cerebellar granule cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);box C/D snoRNP assembly;regulation of transcription, DNA-templated;snoRNA localization
• Cellular component: nucleus;cytoplasm;pre-snoRNP complex
• Molecular function: protein binding;metal ion binding;thyroid hormone receptor binding