UHRF2

ubiquitin like with PHD and ring finger domains 2, the group of Tudor domain containing|PHD finger proteins|Ring finger proteins

Basic information

Region (hg38): 9:6413151-6507056

Links

ENSG00000147854 ∙ NCBI:115426 ∙ OMIM:615211 ∙ HGNC:12557 ∙ Uniprot:Q96PU4 ∙ 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 UHRF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UHRF2 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				1		1
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in UHRF2

This is a list of pathogenic ClinVar variants found in the UHRF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-6413513-T-C		not specified	Uncertain significance (Nov 13, 2024)
9-6413540-A-G		not specified	Uncertain significance (Dec 15, 2023)
9-6413602-G-T		not specified	Uncertain significance (Jan 20, 2023)
9-6421013-A-G			Likely benign (Feb 01, 2023)
9-6421036-C-G		not specified	Uncertain significance (Oct 25, 2023)
9-6421066-C-G		not specified	Uncertain significance (Apr 15, 2024)
9-6421069-G-A		not specified	Uncertain significance (Jun 11, 2024)
9-6421072-T-C		not specified	Uncertain significance (May 06, 2022)
9-6421096-C-T		not specified	Uncertain significance (Jan 30, 2024)
9-6421104-C-T		not specified	Uncertain significance (Aug 13, 2021)
9-6421117-T-C		not specified	Uncertain significance (Feb 28, 2024)
9-6421135-T-C		not specified	Uncertain significance (Apr 27, 2022)
9-6433989-G-T		not specified	Uncertain significance (Jan 26, 2022)
9-6434001-C-G		not specified	Uncertain significance (Nov 15, 2024)
9-6434038-C-A		not specified	Uncertain significance (Mar 07, 2024)
9-6434080-A-G		not specified	Uncertain significance (Jan 16, 2024)
9-6434088-A-C		not specified	Uncertain significance (Aug 02, 2021)
9-6434148-G-A		not specified	Uncertain significance (Sep 12, 2023)
9-6434152-T-C		not specified	Uncertain significance (Jun 16, 2024)
9-6460604-G-A		not specified	Uncertain significance (Apr 06, 2024)
9-6460670-G-A		not specified	Uncertain significance (Aug 06, 2024)
9-6460714-C-G		not specified	Uncertain significance (Mar 23, 2023)
9-6460772-C-T		not specified	Uncertain significance (Jan 23, 2024)
9-6477625-G-A		not specified	Uncertain significance (Aug 01, 2022)
9-6477636-G-C		not specified	Uncertain significance (Jun 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UHRF2	protein_coding	protein_coding	ENST00000276893	16	93904

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000716	125739	0	8	125747	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.32	244	440	0.554	0.0000227	5235
Missense in Polyphen		90	262.04	0.34345		3121
Synonymous	-2.44	187	149	1.25	0.00000739	1532
Loss of Function	5.37	5	43.0	0.116	0.00000233	529

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that is an intermolecular hub protein in the cell cycle network. Through cooperative DNA and histone binding, may contribute to a tighter epigenetic control of gene expression in differentiated cells. Ubiquitinates cyclins, CCND1 and CCNE1, in an apparently phosphorylation-independent manner and induces G1 arrest. Also ubiquitinates PCNP leading to its degradation by the proteasome. E3 SUMO-, but not ubiquitin-, protein ligase for ZNF131. {ECO:0000269|PubMed:12176013, ECO:0000269|PubMed:14741369, ECO:0000269|PubMed:15178429, ECO:0000269|PubMed:15361834, ECO:0000269|PubMed:21952639, ECO:0000269|PubMed:23404503}.
• Disease: DISEASE: Note=Associated with various cancers. DNA copy number loss is found in multiple kinds of malignancies originating from the brain, breast, stomach, kidney, hematopoietic tissue and lung.

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.0576
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.263
• hipred: Y
• hipred_score: 0.825
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uhrf2
• Phenotype: skeleton phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: cell cycle;cell population proliferation;maintenance of DNA methylation;protein ubiquitination;protein sumoylation;cell differentiation;regulation of cell cycle;protein autoubiquitination;positive regulation of cell cycle arrest
• Cellular component: nucleus;nucleoplasm;nuclear heterochromatin
• Molecular function: DNA binding;ubiquitin-protein transferase activity;protein binding;SUMO transferase activity;histone binding;metal ion binding;ubiquitin protein ligase activity