HIVEP3

HIVEP zinc finger 3, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:41506365-42035925

Links

ENSG00000127124 ∙ NCBI:59269 ∙ OMIM:606649 ∙ HGNC:13561 ∙ Uniprot:Q5T1R4 ∙ 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 HIVEP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIVEP3 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				28	21	49
missense			3	11	22	36
nonsense						0
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	5	39	43

Variants in HIVEP3

This is a list of pathogenic ClinVar variants found in the HIVEP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-41510461-G-C		HIVEP3-related disorder	Benign (Mar 23, 2019)
1-41510546-G-A		not specified • HIVEP3-related disorder	Benign (Mar 29, 2016)
1-41510581-C-T		HIVEP3-related disorder	Likely benign (Aug 31, 2020)
1-41510639-C-T			Benign (Aug 02, 2017)
1-41510649-G-A		HIVEP3-related disorder	Benign (Jan 08, 2020)
1-41510657-T-C		not specified • HIVEP3-related disorder	Benign (Mar 29, 2016)
1-41510658-C-T		HIVEP3-related disorder	Likely benign (Feb 21, 2019)
1-41510659-G-A		HIVEP3-related disorder	Benign (Mar 23, 2019)
1-41510674-T-C		HIVEP3-related disorder	Benign (Nov 16, 2019)
1-41510704-C-T		HIVEP3-related disorder	Benign (Feb 21, 2019)
1-41510721-C-T			Likely benign (Oct 01, 2022)
1-41510751-G-T		HIVEP3-related disorder	Likely benign (Aug 13, 2019)
1-41510784-G-A			Likely benign (Oct 01, 2022)
1-41510826-G-A		HIVEP3-related disorder	Likely benign (Apr 23, 2019)
1-41510858-C-T		not specified • HIVEP3-related disorder	Benign (Mar 29, 2016)
1-41510860-C-T		HIVEP3-related disorder	Uncertain significance (Apr 08, 2024)
1-41510904-A-G		HIVEP3-related disorder	Benign (Aug 03, 2017)
1-41510913-G-A		HIVEP3-related disorder	Likely benign (Mar 12, 2019)
1-41510950-C-T		HIVEP3-related disorder	Benign (May 23, 2019)
1-41510981-C-T		HIVEP3-related disorder	Likely benign (Jan 28, 2020)
1-41510994-G-A		HIVEP3-related disorder	Benign (Mar 21, 2019)
1-41511049-C-T		HIVEP3-related disorder	Benign (Jun 04, 2019)
1-41511076-CC-AT		HIVEP3-related disorder	Uncertain significance (Jul 12, 2024)
1-41511246-A-G			Likely benign (Jul 01, 2022)
1-41511257-C-T		HIVEP3-related disorder	Benign (Dec 09, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIVEP3	protein_coding	protein_coding	ENST00000372583	6	529561

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.906	0.0942	125639	0	109	125748	0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	1274	1.40e+3	0.912	0.0000839	15378
Missense in Polyphen		373	526.24	0.70881		5946
Synonymous	-0.873	627	600	1.05	0.0000383	5206
Loss of Function	6.34	15	73.7	0.203	0.00000435	880

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00106	0.00105
Ashkenazi Jewish	0.00477	0.00477
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000223	0.000220
Middle Eastern	0.00	0.00
South Asian	0.000199	0.000196
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role of transcription factor; binds to recognition signal sequences (Rss heptamer) for somatic recombination of immunoglobulin and T-cell receptor gene segments; Binds also to the kappa-B motif of gene such as S100A4, involved in cell progression and differentiation. Kappa-B motif is a gene regulatory element found in promoters and enhancers of genes involved in immunity, inflammation, and growth and that responds to viral antigens, mitogens, and cytokines. Involvement of HIVEP3 in cell growth is strengthened by the fact that its down- regulation promotes cell cycle progression with ultimate formation of multinucleated giant cells. Strongly inhibits TNF-alpha-induced NF-kappa-B activation; Interferes with nuclear factor NF-kappa-B by several mechanisms: as transcription factor, by competing for Kappa-B motif and by repressing transcription in the nucleus; through a non transcriptional process, by inhibiting nuclear translocation of RELA by association with TRAF2, an adapter molecule in the tumor necrosis factor signaling, which blocks the formation of IKK complex. Interaction with TRAF proteins inhibits both NF-Kappa-B-mediated and c-Jun N-terminal kinase/JNK-mediated responses that include apoptosis and proinflammatory cytokine gene expression. Positively regulates the expression of IL2 in T-cell. Essential regulator of adult bone formation. {ECO:0000269|PubMed:11161801}.
• Pathway: Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of RUNX2 expression and activity (Consensus)

Recessive Scores

• pRec: 0.189

Intolerance Scores

• loftool: 0.349
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.21

Haploinsufficiency Scores

• pHI: 0.283
• hipred: Y
• hipred_score: 0.595
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.684

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hivep3
• Phenotype: cellular phenotype; hematopoietic system phenotype; neoplasm; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;skeletal muscle cell differentiation;positive regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding