RNF38

protein-coding

ring finger protein 38, the group of Ring finger proteins

Gene summary

This gene encodes a protein with a coiled-coil motif and a RING-H2 motif (C3H2C2) at its carboxy-terminus. The RING motif is a zinc-binding domain found in a large set of proteins playing roles in diverse cellular processes including oncogenesis, development, signal transduction, and apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

MANE transcript

NM_022781.5

Inheritance

—

ClinVar variants

U:66B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr9:36,336,396-36,487,548

External References & Databases

Ensembl (ENSG00000137075)

Transcript & Mutation Effects

hg38 • Region Span ~151.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RNF38 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022781.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			60 clinvar	1 clinvar		61
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	66	1	0	67

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022781.5	RefSeq	NP_073618.3	12	MANE Select
ENST00000259605.11	Ensembl	ENSP00000259605.6	12	MANE Select
NM_194328.3	RefSeq	NP_919309.1	10	Standard
NM_194329.3	RefSeq	NP_919310.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

male gonad development
protein ubiquitination

Molecular Function

ubiquitin-protein transferase activity
metal ion binding

Cellular Component

nucleus
nucleoplasm
sperm flagellum

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000259605
Coding exons: 12
Length: 151153
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125744
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.56	216	291	0.742	0.0000154	3319
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.776

Gene Damage Prediction

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