ZNHIT3

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

Basic information

Region (hg38): 17:36486628-36499310

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

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 (8 variants)
• not provided (4 variants)
• PEHO syndrome (3 variants)
• not specified (2 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.

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		2
missense		1	7	1		9
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	1	2
Total	0	1	9	4	1

Highest pathogenic variant AF is 0.000414

Variants in ZNHIT3

This is a list of pathogenic ClinVar variants found in the ZNHIT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-36486706-T-A		PEHO syndrome	Uncertain significance (Apr 06, 2018)
17-36486710-T-C		Inborn genetic diseases	Uncertain significance (Mar 24, 2023)
17-36486716-G-A		Inborn genetic diseases	Uncertain significance (Mar 16, 2022)
17-36486720-C-T		PEHO syndrome • ZNHIT3-related disorder	Benign/Likely benign (Sep 27, 2021)
17-36486772-T-G		Inborn genetic diseases	Uncertain significance (Dec 16, 2023)
17-36486779-T-A		Inborn genetic diseases	Uncertain significance (Feb 28, 2024)
17-36486783-C-T			Likely benign (Dec 31, 2019)
17-36486794-G-A			Benign (Dec 31, 2019)
17-36486940-C-T		PEHO syndrome	Likely pathogenic (May 29, 2020)
17-36486954-C-T		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
17-36486964-A-G		Inborn genetic diseases	Uncertain significance (May 04, 2023)
17-36492857-T-C		Inborn genetic diseases	Uncertain significance (Oct 28, 2023)
17-36492878-G-A		Inborn genetic diseases	Likely benign (Aug 11, 2021)
17-36493933-T-C			Likely benign (Dec 31, 2019)
17-36493940-A-G		Inborn genetic diseases	Likely benign (Jul 05, 2023)
17-36493971-AAGAC-A		not specified	Uncertain significance (Sep 06, 2023)
17-36493990-G-T		Inborn genetic diseases	Uncertain significance (Aug 10, 2023)
17-36495236-A-AT		not specified	Uncertain significance (Nov 12, 2020)
17-36495297-G-A		Inborn genetic diseases	Uncertain significance (Aug 04, 2023)
17-36495298-A-G		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
17-36496255-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-36496283-C-T		not specified	Uncertain significance (Dec 06, 2021)
17-36496302-T-C			Likely benign (Sep 01, 2022)
17-36496340-G-A		not specified	Uncertain significance (May 03, 2023)
17-36496369-C-T		not specified	Uncertain significance (Dec 08, 2023)

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