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.

• not_specified (83 variants)

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. These statistics are base on transcript: NM_000181710.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			79	4		83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	4	0

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