RNF39

ring finger protein 39, the group of Ring finger proteins

Basic information

Region (hg38): 6:30070266-30075849

Links

ENSG00000204618 ∙ NCBI:80352 ∙ OMIM:607524 ∙ HGNC:18064 ∙ Uniprot:Q9H2S5 ∙ 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 RNF39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF39 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6			6
Total	0	0	22	3	0

Variants in RNF39

This is a list of pathogenic ClinVar variants found in the RNF39 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30071128-C-G		not specified	Uncertain significance (Dec 11, 2023)
6-30071139-G-A		not specified	Uncertain significance (Dec 15, 2023)
6-30071145-C-G		not specified	Uncertain significance (Mar 17, 2023)
6-30071184-C-T		not specified	Uncertain significance (Oct 27, 2022)
6-30071187-A-G		not specified	Uncertain significance (Aug 28, 2023)
6-30071233-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-30071270-G-A			Likely benign (Jul 01, 2022)
6-30071277-C-A		not specified	Uncertain significance (Mar 15, 2024)
6-30071298-T-C			Likely benign (May 01, 2023)
6-30071434-C-T		not specified	Uncertain significance (Sep 13, 2023)
6-30071455-C-G		not specified	Uncertain significance (Mar 06, 2023)
6-30071560-C-G		not specified	Uncertain significance (Jan 03, 2024)
6-30071628-C-T		not specified	Uncertain significance (Nov 07, 2022)
6-30071632-G-A		not specified	Uncertain significance (May 14, 2024)
6-30073175-T-C		not specified	Uncertain significance (Jan 02, 2024)
6-30073192-T-A		not specified	Uncertain significance (Dec 11, 2023)
6-30075233-A-G		not specified	Likely benign (Aug 12, 2022)
6-30075315-G-C		not specified	Uncertain significance (Nov 09, 2021)
6-30075333-C-T		not specified	Uncertain significance (Mar 01, 2023)
6-30075336-C-G		not specified	Uncertain significance (Aug 02, 2022)
6-30075344-A-C		not specified	Uncertain significance (Jan 04, 2024)
6-30075602-G-C		not specified	Uncertain significance (Mar 29, 2022)
6-30075605-G-A		not specified	Uncertain significance (Jun 07, 2024)
6-30075608-G-T		not specified	Uncertain significance (Apr 22, 2022)
6-30075632-G-T		not specified	Uncertain significance (Sep 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF39	protein_coding	protein_coding	ENST00000244360	4	5622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000202	0.726	125685	2	61	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	163	219	0.746	0.0000111	2570
Missense in Polyphen		27	53.956	0.50041		697
Synonymous	2.42	66	96.2	0.686	0.00000514	927
Loss of Function	1.07	9	13.2	0.682	6.61e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000141
Middle Eastern	0.000544	0.000544
South Asian	0.000229	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in prolonged long term-potentiation (LTP) maintenance. {ECO:0000250}.

Recessive Scores

• pRec: 0.0995

Haploinsufficiency Scores

• pHI: 0.322
• hipred: N
• hipred_score: 0.285
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.269

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf39

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;cytoplasm
• Molecular function: metal ion binding