ZNHIT1

zinc finger HIT-type containing 1, the group of Zinc fingers HIT-type|SRCAP complex

Basic information

Region (hg38): 7:101218165-101224190

Previous symbols: [ "ZNFN4A1" ]

Links

ENSG00000106400 ∙ NCBI:10467 ∙ OMIM:618617 ∙ HGNC:21688 ∙ Uniprot:O43257 ∙ 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 ZNHIT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNHIT1 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			12			12
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	13	0	1

Variants in ZNHIT1

This is a list of pathogenic ClinVar variants found in the ZNHIT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-101218171-T-C			Benign (May 19, 2019)
7-101218196-A-G			Uncertain significance (Jun 03, 2019)
7-101222607-G-A		not specified	Uncertain significance (Nov 09, 2023)
7-101222651-C-T		not specified	Uncertain significance (Oct 05, 2023)
7-101222652-G-A		not specified	Uncertain significance (Apr 28, 2022)
7-101222669-C-T		not specified	Uncertain significance (Jun 24, 2022)
7-101222762-G-A		not specified	Uncertain significance (Feb 27, 2023)
7-101222766-C-T		not specified	Uncertain significance (Apr 19, 2023)
7-101223555-A-T		not specified	Uncertain significance (Apr 06, 2023)
7-101223716-C-T		not specified	Uncertain significance (Jun 29, 2022)
7-101223725-C-A		not specified	Uncertain significance (Dec 28, 2022)
7-101223730-C-T		not specified	Uncertain significance (Aug 01, 2022)
7-101223752-C-T		not specified	Uncertain significance (Jan 30, 2024)
7-101223799-C-T		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNHIT1	protein_coding	protein_coding	ENST00000305105	5	6523

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000236	0.301	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	76	109	0.697	0.00000784	984
Missense in Polyphen		15	27.803	0.53951		299
Synonymous	-0.202	45	43.3	1.04	0.00000282	310
Loss of Function	0.237	9	9.80	0.918	5.89e-7	96

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00111
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000109	0.000109
South Asian	0.0000982	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to play a role in p53-mediated apoptosis induction. Binds to NR1D2 and relieves it of its inhibitory effect on the transcription of APOC3 without affecting its DNA-binding activity. {ECO:0000269|PubMed:17380123, ECO:0000269|PubMed:17892483}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.545
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.688
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.264

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Znhit1

Gene ontology

• Biological process: regulation of histone deacetylation;histone exchange
• Cellular component: Swr1 complex;nucleus;nucleoplasm
• Molecular function: protein binding;nucleosome binding;histone deacetylase binding;metal ion binding