RNF40

ring finger protein 40, the group of Ring finger proteins

Basic information

Region (hg38): 16:30761745-30776307

Links

ENSG00000103549 ∙ NCBI:9810 ∙ OMIM:607700 ∙ HGNC:16867 ∙ Uniprot:O75150 ∙ 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 RNF40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF40 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				2	1	3
missense			44	1		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	44	3	2

Variants in RNF40

This is a list of pathogenic ClinVar variants found in the RNF40 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30762620-G-C		not specified	Uncertain significance (Jun 21, 2023)
16-30763143-A-G		not specified	Uncertain significance (Mar 08, 2024)
16-30763169-C-T		not specified	Uncertain significance (Mar 19, 2024)
16-30763203-T-A		not specified	Uncertain significance (Sep 27, 2022)
16-30763222-G-A		not specified	Likely benign (Mar 07, 2024)
16-30763497-C-T		not specified	Uncertain significance (Oct 27, 2022)
16-30763508-C-T		not specified	Uncertain significance (Oct 06, 2021)
16-30764192-G-C		not specified	Uncertain significance (Apr 25, 2023)
16-30764349-C-T		not specified	Uncertain significance (Jun 16, 2023)
16-30764350-G-A		not specified	Likely benign (Nov 22, 2022)
16-30764371-G-A		not specified	Uncertain significance (Jun 30, 2022)
16-30764383-G-A		not specified	Uncertain significance (Jul 14, 2021)
16-30764383-G-C		not specified	Uncertain significance (Mar 12, 2024)
16-30764980-G-A		not specified	Uncertain significance (Jan 04, 2022)
16-30765022-C-T		not specified	Uncertain significance (Feb 06, 2023)
16-30766215-G-A		not specified	Uncertain significance (Oct 26, 2021)
16-30766270-T-A		not specified	Uncertain significance (Mar 23, 2022)
16-30766274-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-30766394-C-A		not specified	Uncertain significance (Apr 08, 2024)
16-30766428-A-G		not specified	Uncertain significance (Jan 10, 2022)
16-30766449-T-A		not specified	Uncertain significance (Nov 30, 2021)
16-30766518-C-T		not specified	Uncertain significance (Sep 07, 2022)
16-30766546-C-T			Likely benign (Mar 29, 2018)
16-30766813-C-T		not specified	Uncertain significance (Nov 15, 2021)
16-30766814-G-T		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF40	protein_coding	protein_coding	ENST00000324685	19	14563

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000129	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	439	630	0.697	0.0000422	6435
Missense in Polyphen		62	156.21	0.3969		1712
Synonymous	1.18	223	247	0.904	0.0000144	2032
Loss of Function	6.27	8	60.8	0.132	0.00000395	608

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000308	0.000304
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000781	0.000756
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role in histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes. {ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:19410543}.
• Pathway: ATM Signaling Network in Development and Disease;Post-translational protein modification;Metabolism of proteins;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.457
• rvis_EVS: -1.99
• rvis_percentile_EVS: 1.76

Haploinsufficiency Scores

• pHI: 0.320
• hipred: Y
• hipred_score: 0.785
• ghis: 0.634

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf40

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;regulation of mitotic cell cycle;histone monoubiquitination;protein ubiquitination;histone H2B ubiquitination;response to peptide hormone;negative regulation of mRNA polyadenylation;positive regulation of proteasomal protein catabolic process;positive regulation of protein polyubiquitination;positive regulation of histone H2B ubiquitination
• Cellular component: ubiquitin ligase complex;nucleus;nucleoplasm;cytosol;membrane;extrinsic component of membrane;HULC complex;neuron projection;axon terminus
• Molecular function: mRNA 3'-UTR binding;ubiquitin-protein transferase activity;protein binding;syntaxin-1 binding;ubiquitin conjugating enzyme binding;ubiquitin protein ligase binding;protein homodimerization activity;protein-containing complex binding;metal ion binding