ZNHIT2

zinc finger HIT-type containing 2, the group of Zinc fingers HIT-type

Basic information

Region (hg38): 11:65116403-65117701

Previous symbols: [ "C11orf5" ]

Links

ENSG00000174276 ∙ NCBI:741 ∙ OMIM:604575 ∙ HGNC:1177 ∙ Uniprot:Q9UHR6 ∙ 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 ZNHIT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNHIT2 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			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	1	2

Variants in ZNHIT2

This is a list of pathogenic ClinVar variants found in the ZNHIT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65116486-C-T		not specified	Uncertain significance (Oct 17, 2023)
11-65116530-A-G		not specified	Uncertain significance (Apr 07, 2022)
11-65116546-C-T		not specified	Uncertain significance (Jan 26, 2022)
11-65116561-G-A		not specified	Uncertain significance (May 28, 2024)
11-65116566-C-G		not specified	Uncertain significance (Jan 23, 2023)
11-65116582-C-T		not specified	Uncertain significance (Jun 27, 2022)
11-65116618-A-T		not specified	Uncertain significance (Sep 26, 2022)
11-65116633-G-T		not specified	Uncertain significance (Nov 29, 2023)
11-65116662-T-G		not specified	Uncertain significance (Apr 09, 2024)
11-65116663-C-A		not specified	Uncertain significance (Apr 27, 2022)
11-65116698-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-65116743-C-T		not specified	Uncertain significance (Apr 19, 2024)
11-65116752-T-C		not specified	Uncertain significance (Jun 02, 2024)
11-65116780-G-A		not specified	Uncertain significance (May 23, 2024)
11-65116803-C-T		not specified	Uncertain significance (May 31, 2023)
11-65116809-C-G		not specified	Uncertain significance (May 16, 2023)
11-65116834-C-T		not specified	Uncertain significance (Aug 22, 2022)
11-65116897-C-A		not specified	Uncertain significance (Jan 31, 2022)
11-65116902-A-G		not specified	Uncertain significance (May 20, 2024)
11-65116921-G-A		not specified	Uncertain significance (Dec 27, 2022)
11-65116972-G-C		not specified	Uncertain significance (Dec 21, 2022)
11-65116994-G-T		not specified	Uncertain significance (Feb 17, 2022)
11-65117080-C-G		not specified	Uncertain significance (May 20, 2024)
11-65117100-G-A		not specified	Uncertain significance (Aug 22, 2023)
11-65117112-A-G		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNHIT2	protein_coding	protein_coding	ENST00000310597	1	1296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000225	0.510	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0281	224	223	1.01	0.0000120	2449
Missense in Polyphen		95	103.42	0.91857		1189
Synonymous	-1.56	127	107	1.19	0.00000596	929
Loss of Function	0.589	8	10.0	0.799	5.25e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.117

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.201
• hipred: N
• hipred_score: 0.312
• ghis: 0.536

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.768

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Znhit2

Gene ontology

• Molecular function: metal ion binding