HIVEP2

HIVEP zinc finger 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 6:142751469-142956698

Links

ENSG00000010818

∙ NCBI:3097 ∙ OMIM:143054 ∙ HGNC:4921 ∙ Uniprot:P31629 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

intellectual disability, autosomal dominant 43 (Strong), mode of inheritance: AD
autosomal dominant non-syndromic intellectual disability (Supportive), mode of inheritance: AD
intellectual disability, autosomal dominant 43 (Strong), mode of inheritance: AD
intellectual disability, autosomal dominant 43 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mental retardation, autosomal dominant 43	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	23020937; 26153216; 27003583

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HIVEP2 gene.

not_provided (961 variants)
Inborn_genetic_diseases (289 variants)
Intellectual_disability,_autosomal_dominant_43 (161 variants)
HIVEP2-related_disorder (87 variants)
not_specified (60 variants)
Intellectual_disability (8 variants)
See_cases (8 variants)
Angelman_syndrome-like (2 variants)
Neurodevelopmental_disorder (1 variants)
Epilepsy (1 variants)
Congenital_ocular_coloboma (1 variants)
Autism_spectrum_disorder (1 variants)
Neurodevelopmental_delay (1 variants)
Vascular_disorder (1 variants)
HP:0000750%3B_HP:0001263 (1 variants)
Intellectual_disability,_autosomal_dominant_13 (1 variants)
HIVEP2-related_syndromic_intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIVEP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006734.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	210 clinvar	105 clinvar	318
missense	1 clinvar	3 clinvar	532 clinvar	294 clinvar	31 clinvar	861
nonsense	23 clinvar	2 clinvar	1 clinvar			26
start loss						0
frameshift	25 clinvar	13 clinvar	2 clinvar	1 clinvar		41
splice donor/acceptor (+/-2bp)		2 clinvar	1 clinvar			3
Total	49	20	539	505	136

Highest pathogenic variant AF is 0.00000136811

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIVEP2	protein_coding	protein_coding	ENST00000367603	6	193735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.60e-12	124789	0	7	124796	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	1129	1.32e+3	0.858	0.0000739	16010
Missense in Polyphen		317	516.63	0.61359		6391
Synonymous	-0.942	547	520	1.05	0.0000319	4889
Loss of Function	8.02	2	78.8	0.0254	0.00000432	1068

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000130	0.000129
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000354	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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 HIV1. 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, somatostatin receptor II, and interferon- beta genes. It may act in T-cell activation.;
Disease: DISEASE: Mental retardation, autosomal dominant 43 (MRD43) [MIM:616977]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD43 patients manifest developmental delay, intellectual disability, hypotonia, and dysmorphic features. {ECO:0000269|PubMed:23020937, ECO:0000269|PubMed:26153216}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.156

Intolerance Scores

loftool: 0.0160
rvis_EVS: -2.2
rvis_percentile_EVS: 1.37

Haploinsufficiency Scores

pHI: 0.579
hipred: Y
hipred_score: 0.825
ghis: 0.548

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.852

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Hivep2
Phenotype: hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype;

Gene ontology

Biological process: regulation of transcription by RNA polymerase II
Cellular component: nucleoplasm
Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding