ZNRF2

zinc and ring finger 2, the group of MicroRNA protein coding host genes|Ring finger proteins

Basic information

Region (hg38): 7:30284597-30367689

Links

ENSG00000180233 ∙ NCBI:223082 ∙ OMIM:612061 ∙ HGNC:22316 ∙ Uniprot:Q8NHG8 ∙ 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 ZNRF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNRF2 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in ZNRF2

This is a list of pathogenic ClinVar variants found in the ZNRF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-30285376-G-A		not specified	Uncertain significance (May 30, 2024)
7-30285401-C-T		not specified	Uncertain significance (Sep 23, 2023)
7-30285442-G-C		not specified	Uncertain significance (Jul 19, 2022)
7-30285452-A-G		not specified	Uncertain significance (May 20, 2024)
7-30285539-C-A		not specified	Uncertain significance (Mar 29, 2023)
7-30285558-G-C			Likely benign (Oct 01, 2023)
7-30285560-C-T		not specified	Uncertain significance (Jan 24, 2024)
7-30285623-G-C		not specified	Uncertain significance (Apr 07, 2023)
7-30285644-C-A		not specified	Uncertain significance (Oct 26, 2022)
7-30285650-A-G		not specified	Uncertain significance (Feb 12, 2024)
7-30285655-C-A		not specified	Uncertain significance (Apr 07, 2023)
7-30285661-A-G		not specified	Uncertain significance (Feb 10, 2022)
7-30285686-C-A		not specified	Uncertain significance (May 04, 2022)
7-30285736-G-A		not specified	Uncertain significance (Nov 27, 2023)
7-30323690-A-G		not specified	Uncertain significance (Aug 10, 2023)
7-30323705-T-C		not specified	Uncertain significance (Apr 17, 2023)
7-30355745-G-C		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNRF2	protein_coding	protein_coding	ENST00000323037	4	128196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0723	0.878	125710	0	4	125714	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	42	66.5	0.632	0.00000309	1512
Missense in Polyphen		9	25.774	0.34919		393
Synonymous	-1.19	32	24.5	1.31	0.00000109	510
Loss of Function	1.66	3	8.10	0.370	5.38e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000916	0.0000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000660	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the establishment and maintenance of neuronal transmission and plasticity via its ubiquitin ligase activity. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates. {ECO:0000269|PubMed:14561866}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.114

Haploinsufficiency Scores

• pHI: 0.0713
• hipred: N
• hipred_score: 0.320
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.542

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Znrf2

Gene ontology

• Biological process: protein polyubiquitination
• Cellular component: cytoplasm;lysosomal membrane;cytosol;plasma membrane;endosome membrane;cell junction;cytoplasmic vesicle membrane;protein-containing complex;presynaptic membrane
• Molecular function: ubiquitin-protein transferase activity;metal ion binding;ubiquitin protein ligase activity