ZNHIT6

zinc finger HIT-type containing 6, the group of Zinc fingers HIT-type

Basic information

Region (hg38): 1:85649417-85708433

Previous symbols: [ "C1orf181" ]

Links

ENSG00000117174 ∙ NCBI:54680 ∙ ∙ HGNC:26089 ∙ Uniprot:Q9NWK9 ∙ 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 ZNHIT6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNHIT6 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in ZNHIT6

This is a list of pathogenic ClinVar variants found in the ZNHIT6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-85657873-T-C		not specified	Likely benign (Jul 19, 2023)
1-85657892-C-T		not specified	Uncertain significance (Jun 13, 2023)
1-85657901-T-C		not specified	Uncertain significance (Sep 26, 2023)
1-85657957-T-A		not specified	Uncertain significance (Aug 11, 2022)
1-85677296-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-85677297-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-85678708-G-A		not specified	Uncertain significance (Feb 13, 2024)
1-85678755-T-C		not specified	Uncertain significance (Feb 14, 2023)
1-85702202-T-C		not specified	Uncertain significance (Aug 02, 2021)
1-85702245-T-C		not specified	Uncertain significance (Apr 07, 2022)
1-85706079-T-C		not specified	Uncertain significance (May 23, 2024)
1-85706127-T-C		not specified	Uncertain significance (Jul 08, 2022)
1-85706130-G-A		not specified	Uncertain significance (Feb 10, 2023)
1-85706262-C-G		not specified	Uncertain significance (Jun 05, 2023)
1-85706274-C-A		not specified	Uncertain significance (Nov 17, 2023)
1-85706288-T-C		not specified	Likely benign (Apr 15, 2024)
1-85706305-C-T		not specified	Uncertain significance (May 16, 2024)
1-85706338-T-C		not specified	Uncertain significance (Jun 13, 2024)
1-85706463-C-T		not specified	Uncertain significance (Jun 27, 2022)
1-85707632-G-A		not specified	Uncertain significance (May 31, 2023)
1-85707695-G-A		not specified	Uncertain significance (Nov 07, 2023)
1-85707708-T-G		not specified	Uncertain significance (Jun 22, 2023)
1-85707732-C-T		not specified	Uncertain significance (Apr 01, 2024)
1-85707769-T-C		not specified	Uncertain significance (Apr 13, 2022)
1-85707804-T-C		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNHIT6	protein_coding	protein_coding	ENST00000370574	10	59011

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.53e-12	0.243	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.296	233	246	0.947	0.0000118	3120
Missense in Polyphen		48	49.914	0.96166		653
Synonymous	0.274	81	84.2	0.962	0.00000391	819
Loss of Function	0.932	20	25.0	0.799	0.00000128	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000346	0.000345
Ashkenazi Jewish	0.00	0.00
East Asian	0.000334	0.000326
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.000334	0.000326
South Asian	0.000266	0.000261
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for box C/D snoRNAs accumulation involved in snoRNA processing, snoRNA transport to the nucleolus and ribosome biogenesis. {ECO:0000269|PubMed:17636026}.

Recessive Scores

• pRec: 0.0832

Intolerance Scores

• loftool: 0.955
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.221
• hipred: N
• hipred_score: 0.173
• ghis: 0.609

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.278

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Znhit6

Gene ontology

• Biological process: maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);box C/D snoRNP assembly;snoRNA localization;protein complex oligomerization
• Cellular component: nucleus;extracellular exosome;pre-snoRNP complex
• Molecular function: TFIID-class transcription factor complex binding;protein binding;enzyme binding;identical protein binding;metal ion binding;ATPase binding