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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:O43567AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

  • developmental and epileptic encephalopathy, 73 (Limited), 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 (143 variants)
  • Developmental and epileptic encephalopathy, 73 (10 variants)
  • Inborn genetic diseases (7 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 1 18 4 23
missense 2 74 7 2 85
nonsense 1 2 4 7
start loss 0
frameshift 2 3 5
inframe indel 2 2
splice variant 3 12 2 17
non coding 2 11 2 15
Total 3 4 89 48 10

Variants in RNF13

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

Position Type Phenotype Significance ClinVar
3-149846042-G-A Uncertain significance (Aug 26, 2021)link
3-149846060-G-A Uncertain significance (Jun 22, 2021)link
3-149846069-G-A Uncertain significance (Oct 18, 2022)link
3-149846070-T-A Uncertain significance (May 17, 2022)link
3-149846072-T-C Uncertain significance (Mar 29, 2023)link
3-149846078-A-G Uncertain significance (Oct 13, 2022)link
3-149846083-G-T Uncertain significance (Aug 27, 2021)link
3-149846111-C-A Uncertain significance (Aug 31, 2021)link
3-149846115-T-A Inborn genetic diseases Uncertain significance (Jun 09, 2022)link
3-149846125-A-G Likely benign (Sep 27, 2022)link
3-149846132-A-G Developmental and epileptic encephalopathy, 73 Uncertain significance (-)link
3-149846149-A-G Likely benign (Sep 06, 2022)link
3-149846158-T-C Likely benign (Mar 25, 2021)link
3-149872014-C-T Likely benign (Sep 15, 2022)link
3-149872032-T-G Uncertain significance (Sep 27, 2022)link
3-149872045-CAA-C Uncertain significance (Jul 12, 2022)link
3-149872049-A-G Likely benign (Oct 24, 2022)link
3-149872051-C-A Uncertain significance (Jul 12, 2022)link
3-149872066-A-AGGC Uncertain significance (Oct 13, 2022)link
3-149872071-A-G Uncertain significance (Feb 14, 2022)link
3-149872086-G-A Uncertain significance (Sep 24, 2021)link
3-149872095-A-T Developmental and epileptic encephalopathy, 73 Uncertain significance (May 06, 2021)link
3-149872100-A-G Likely benign (Aug 16, 2022)link
3-149872107-A-T Inborn genetic diseases Uncertain significance (Jan 10, 2023)link
3-149872115-C-T Likely benign (Aug 01, 2023)link

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