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GeneBe

RNF13

ring finger protein 13, the group of Ring finger proteins

Basic information

Region (hg38): 3:149812769-149962139

Links

ENSG00000082996NCBI:11342OMIM:609247HGNC:10057Uniprot:O43567AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • developmental and epileptic encephalopathy, 73 (Limited), mode of inheritance: AD
  • developmental and epileptic encephalopathy, 73 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Developmental and epileptic encephalopathy 73ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic; Craniofacial; Neurologic30595371

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF13 gene.

  • not provided (161 variants)
  • Inborn genetic diseases (10 variants)
  • Developmental and epileptic encephalopathy, 73 (8 variants)
  • RNF13-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF13 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
clinvar
27
clinvar
3
clinvar
31
missense
83
clinvar
4
clinvar
2
clinvar
89
nonsense
1
clinvar
1
clinvar
3
clinvar
5
start loss
0
frameshift
2
clinvar
5
clinvar
7
inframe indel
3
clinvar
3
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
4
11
2
17
non coding
2
clinvar
12
clinvar
2
clinvar
16
Total 1 3 98 43 7

Variants in RNF13

This is a list of pathogenic ClinVar variants found in the RNF13 region.

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

Position Type Phenotype Significance ClinVar
3-149846041-A-G Likely benign (Dec 12, 2023)2693606
3-149846042-G-A Uncertain significance (Jan 06, 2021)1466650
3-149846042-G-C Uncertain significance (Oct 17, 2023)2897437
3-149846051-A-G Uncertain significance (Jan 05, 2023)2874551
3-149846060-G-A Uncertain significance (Jun 22, 2021)1329512
3-149846067-A-G Uncertain significance (Nov 24, 2023)2881554
3-149846069-G-A Benign (Nov 27, 2023)1518183
3-149846070-T-A Uncertain significance (Dec 27, 2022)1995831
3-149846072-T-C Uncertain significance (Mar 29, 2023)2581970
3-149846076-C-T Uncertain significance (Sep 15, 2023)2778159
3-149846078-A-G Uncertain significance (Jan 18, 2024)1421910
3-149846083-G-T Uncertain significance (Dec 13, 2023)1492876
3-149846111-C-A Uncertain significance (Jan 11, 2021)1493452
3-149846115-T-A Inborn genetic diseases Uncertain significance (Jul 25, 2023)2374666
3-149846116-G-A Likely benign (Dec 30, 2023)3009953
3-149846125-A-G Likely benign (Feb 02, 2023)2126986
3-149846132-A-G Developmental and epileptic encephalopathy, 73 Uncertain significance (-)2585441
3-149846145-G-T Uncertain significance (Dec 23, 2023)2705077
3-149846149-A-G Likely benign (Sep 06, 2022)1940487
3-149846158-T-C Likely benign (Feb 08, 2023)1614636
3-149852546-G-A RNF13-related condition Uncertain significance (Jan 04, 2024)3047514
3-149872014-C-T Likely benign (May 01, 2023)1555678
3-149872032-T-G Uncertain significance (Oct 03, 2023)1926869
3-149872045-CAA-C Uncertain significance (Aug 10, 2023)1426617
3-149872049-A-G Likely benign (Jan 10, 2024)1408043

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNF13protein_codingprotein_codingENST00000344229 9149432
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0004030.9631257320121257440.0000477
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9011581930.8180.000009192506
Missense in Polyphen3957.70.67591788
Synonymous-0.6187770.41.090.00000353705
Loss of Function1.86816.00.4996.69e-7244

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001200.000120
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00005460.0000527
Middle Eastern0.00005440.0000544
South Asian0.00006770.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: E3 ubiquitin-protein ligase that may play a role in controlling cell proliferation. {ECO:0000269|PubMed:18794910}.;

Recessive Scores

pRec
0.0875

Intolerance Scores

loftool
0.732
rvis_EVS
-0.01
rvis_percentile_EVS
53.51

Haploinsufficiency Scores

pHI
0.397
hipred
N
hipred_score
0.204
ghis
0.513

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.866

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rnf13
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype;

Gene ontology

Biological process
ubiquitin-dependent protein catabolic process;protein autoubiquitination
Cellular component
Golgi membrane;nuclear inner membrane;nucleoplasm;lysosomal membrane;endoplasmic reticulum membrane;cytosol;integral component of membrane;late endosome membrane;intracellular membrane-bounded organelle
Molecular function
ubiquitin-protein transferase activity;protein binding;metal ion binding;ubiquitin protein ligase activity