RNF38

ring finger protein 38, the group of Ring finger proteins

Basic information

Region (hg38): 9:36336396-36487548

Links

ENSG00000137075 ∙ NCBI:152006 ∙ OMIM:612488 ∙ HGNC:18052 ∙ Uniprot:Q9H0F5 ∙ 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 RNF38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF38 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in RNF38

This is a list of pathogenic ClinVar variants found in the RNF38 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-36339765-C-T		not specified	Uncertain significance (Jan 19, 2022)
9-36344850-T-C		not specified	Uncertain significance (Jan 16, 2025)
9-36344862-T-C		not specified	Uncertain significance (May 08, 2023)
9-36351145-A-C		not specified	Uncertain significance (Jan 16, 2025)
9-36351165-T-G		not specified	Uncertain significance (Feb 23, 2023)
9-36352811-C-T		not specified	Uncertain significance (Mar 03, 2025)
9-36352827-G-A		not specified	Uncertain significance (Apr 26, 2023)
9-36352848-G-T		not specified	Uncertain significance (Dec 09, 2023)
9-36353193-G-A		not specified	Uncertain significance (Sep 17, 2021)
9-36353204-T-C		not specified	Uncertain significance (May 03, 2023)
9-36353244-G-C		not specified	Uncertain significance (Jul 05, 2023)
9-36353244-G-T		not specified	Uncertain significance (Nov 26, 2024)
9-36356329-G-C		not specified	Uncertain significance (May 25, 2022)
9-36356387-A-T		not specified	Uncertain significance (Feb 14, 2023)
9-36356388-T-A		not specified	Uncertain significance (Jan 17, 2024)
9-36356410-A-G		not specified	Uncertain significance (May 27, 2022)
9-36356413-T-C		not specified	Uncertain significance (Mar 04, 2024)
9-36356455-C-T		not specified	Uncertain significance (Sep 25, 2024)
9-36357779-G-A		not specified	Uncertain significance (Apr 07, 2023)
9-36357780-G-C		not specified	Uncertain significance (Jan 07, 2025)
9-36357819-C-T		not specified	Uncertain significance (Dec 07, 2021)
9-36357822-C-G		not specified	Uncertain significance (Aug 02, 2022)
9-36357849-T-C		not specified	Uncertain significance (Sep 27, 2022)
9-36369738-A-G		not specified	Uncertain significance (Jan 28, 2025)
9-36369784-G-A		not specified	Uncertain significance (Aug 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF38	protein_coding	protein_coding	ENST00000259605	12	151153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000466	125734	0	10	125744	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	216	291	0.742	0.0000154	3319
Missense in Polyphen		36	70.504	0.51061		793
Synonymous	0.244	95	98.1	0.969	0.00000476	1054
Loss of Function	5.13	1	32.6	0.0307	0.00000212	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000623	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an E3 ubiquitin-protein ligase able to ubiquitinate p53/TP53 which promotes its relocalization to discrete foci associated with PML nuclear bodies. Exhibits preference for UBE2D2 as a E2 enzyme. {ECO:0000269|PubMed:23973461}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.384
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.557
• hipred: Y
• hipred_score: 0.654
• ghis: 0.640

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.776

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf38
• Phenotype: vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); skeleton phenotype; hearing/vestibular/ear phenotype

Gene ontology

• Biological process: male gonad development;protein ubiquitination
• Cellular component: nucleus;nucleoplasm;sperm flagellum
• Molecular function: ubiquitin-protein transferase activity;metal ion binding