HIVEP1

HIVEP zinc finger 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 6:12008761-12164999

Previous symbols: [ "ZNF40" ]

Links

ENSG00000095951 ∙ NCBI:3096 ∙ OMIM:194540 ∙ HGNC:4920 ∙ Uniprot:P15822 ∙ 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 HIVEP1 gene.

• Inborn genetic diseases (117 variants)
• not provided (43 variants)
• not specified (4 variants)
• HIVEP1-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIVEP1 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				13	7	20
missense			112	16	16	144
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	112	29	23

Variants in HIVEP1

This is a list of pathogenic ClinVar variants found in the HIVEP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-12015643-A-G			Likely benign (Apr 01, 2022)
6-12015666-G-A		not specified	Uncertain significance (Sep 27, 2022)
6-12089215-T-G		not specified	Uncertain significance (Mar 14, 2023)
6-12120048-G-A		not specified	Likely benign (Jun 24, 2022)
6-12120057-C-T			Likely benign (Jul 15, 2018)
6-12120073-C-G		not specified	Uncertain significance (Jan 29, 2024)
6-12120093-A-C		not specified	Uncertain significance (Dec 26, 2023)
6-12120204-C-G		not specified	Uncertain significance (Oct 04, 2022)
6-12120226-G-A		not specified	Uncertain significance (Oct 11, 2023)
6-12120275-T-A		not specified	Uncertain significance (Feb 10, 2022)
6-12120303-A-G			Benign (Dec 31, 2019)
6-12120327-G-A		not specified	Uncertain significance (Nov 08, 2022)
6-12120419-C-T			Benign (Dec 31, 2019)
6-12120431-A-G			Likely benign (Jun 01, 2022)
6-12120516-A-G		not specified	Uncertain significance (Jul 09, 2021)
6-12120573-A-C		HIVEP1-related disorder	Uncertain significance (Sep 03, 2023)
6-12120679-A-G		not specified	Uncertain significance (Dec 06, 2021)
6-12120691-A-G		not specified	Uncertain significance (Jun 16, 2023)
6-12120710-A-G		HIVEP1-related disorder	Likely benign (Aug 29, 2022)
6-12120732-A-C		not specified	Uncertain significance (Apr 28, 2022)
6-12120852-G-T		not specified	Uncertain significance (Feb 08, 2023)
6-12120880-C-T			Benign (Dec 31, 2019)
6-12120898-C-T		not specified	Uncertain significance (Oct 05, 2022)
6-12120946-A-C		not specified	Uncertain significance (Oct 05, 2023)
6-12121068-A-C		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIVEP1	protein_coding	protein_coding	ENST00000379388	8	156238

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.52e-8	124789	0	19	124808	0.0000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.328	1409	1.44e+3	0.976	0.0000774	17710
Missense in Polyphen		338	464.48	0.7277		5735
Synonymous	-0.358	587	576	1.02	0.0000346	5545
Loss of Function	7.66	8	83.6	0.0957	0.00000463	1074

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000122
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000885	0.0000883
Middle Eastern	0.000111	0.000111
South Asian	0.0000659	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein specifically binds to the DNA sequence 5'- GGGACTTTCC-3' which is found in the enhancer elements of numerous viral promoters such as those of SV40, CMV, or HIV-1. In addition, related sequences are found in the enhancer elements of a number of cellular promoters, including those of the class I MHC, interleukin-2 receptor, and interferon-beta genes. It may act in T-cell activation. Involved in activating HIV-1 gene expression. Isoform 2 and isoform 3 also bind to the IPCS (IRF1 and p53 common sequence) DNA sequence in the promoter region of interferon regulatory factor 1 and p53 genes and are involved in transcription regulation of these genes. Isoform 2 does not activate HIV-1 gene expression. Isoform 2 and isoform 3 may be involved in apoptosis.

Intolerance Scores

• loftool: 0.339
• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.09

Haploinsufficiency Scores

• pHI: 0.184
• hipred: Y
• hipred_score: 0.538
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.721

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hivep1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;mitochondrion;nuclear body
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding