ZNRF4

zinc and ring finger 4, the group of Ring finger proteins

Basic information

Region (hg38): 19:5455417-5456856

Links

ENSG00000105428 ∙ NCBI:148066 ∙ OMIM:612063 ∙ HGNC:17726 ∙ Uniprot:Q8WWF5 ∙ 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 ZNRF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNRF4 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						0
missense			55	4		59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	4	0

Variants in ZNRF4

This is a list of pathogenic ClinVar variants found in the ZNRF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-5455501-T-G		not specified	Uncertain significance (Oct 04, 2024)
19-5455508-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-5455526-G-C		not specified	Uncertain significance (Sep 26, 2022)
19-5455597-C-T		not specified	Uncertain significance (Apr 01, 2024)
19-5455606-C-G		not specified	Uncertain significance (Nov 21, 2024)
19-5455612-C-T		not specified	Uncertain significance (Feb 08, 2025)
19-5455627-C-T		not specified	Likely benign (Jan 03, 2024)
19-5455693-C-T		not specified	Uncertain significance (Sep 30, 2021)
19-5455694-G-A		not specified	Uncertain significance (Dec 09, 2024)
19-5455708-T-G		not specified	Uncertain significance (Dec 20, 2024)
19-5455714-C-T		not specified	Uncertain significance (Jun 05, 2024)
19-5455732-G-A		not specified	Uncertain significance (Jun 29, 2023)
19-5455793-G-A		not specified	Uncertain significance (Jul 26, 2021)
19-5455798-G-A		not specified	Likely benign (Oct 30, 2023)
19-5455807-G-A		not specified	Uncertain significance (Nov 15, 2024)
19-5455829-T-C		not specified	Uncertain significance (Feb 14, 2023)
19-5455841-C-T		not specified	Uncertain significance (Jan 29, 2024)
19-5455877-T-A		not specified	Uncertain significance (Nov 11, 2024)
19-5455893-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-5455925-T-C		not specified	Uncertain significance (Dec 11, 2024)
19-5455927-G-A		not specified	Uncertain significance (Nov 27, 2023)
19-5455928-A-G		not specified	Uncertain significance (Jan 04, 2024)
19-5455928-A-T		not specified	Uncertain significance (Oct 25, 2024)
19-5455948-C-T		not specified	Uncertain significance (Jul 06, 2021)
19-5455949-G-A		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNRF4	protein_coding	protein_coding	ENST00000222033	1	1442

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.489	0.439	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.245	280	292	0.960	0.0000218	2671
Missense in Polyphen		55	68.564	0.80217		671
Synonymous	-1.11	158	141	1.12	0.0000118	945
Loss of Function	1.26	0	1.84	0.00	7.93e-8	18

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which specifically induces ubiquitination and proteasomal degradation of CANX within the endoplasmic reticulum (PubMed:21205830). Could have a role in spermatogenesis (By similarity). {ECO:0000250|UniProtKB:Q9DAH2, ECO:0000269|PubMed:21205830}.

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• loftool: 0.465
• rvis_EVS: 1.65
• rvis_percentile_EVS: 96.21

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.203
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.246

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Znrf4

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: protein binding;metal ion binding;ubiquitin protein ligase activity