RNF13
ring finger protein 13, the group of Ring finger proteins
Basic information
Region (hg38): 3:149812769-149962139
Links
Phenotypes
GenCC
Source:
- developmental and epileptic encephalopathy, 73 (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Developmental and epileptic encephalopathy 73 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Audiologic/Otolaryngologic; Craniofacial; Neurologic | 30595371 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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) | |||
3-149846060-G-A | Uncertain significance (Jun 22, 2021) | |||
3-149846069-G-A | Uncertain significance (Oct 18, 2022) | |||
3-149846070-T-A | Uncertain significance (May 17, 2022) | |||
3-149846072-T-C | Uncertain significance (Mar 29, 2023) | |||
3-149846078-A-G | Uncertain significance (Oct 13, 2022) | |||
3-149846083-G-T | Uncertain significance (Aug 27, 2021) | |||
3-149846111-C-A | Uncertain significance (Aug 31, 2021) | |||
3-149846115-T-A | Inborn genetic diseases | Uncertain significance (Jun 09, 2022) | ||
3-149846125-A-G | Likely benign (Sep 27, 2022) | |||
3-149846132-A-G | Developmental and epileptic encephalopathy, 73 | Uncertain significance (-) | ||
3-149846149-A-G | Likely benign (Sep 06, 2022) | |||
3-149846158-T-C | Likely benign (Mar 25, 2021) | |||
3-149872014-C-T | Likely benign (Sep 15, 2022) | |||
3-149872032-T-G | Uncertain significance (Sep 27, 2022) | |||
3-149872045-CAA-C | Uncertain significance (Jul 12, 2022) | |||
3-149872049-A-G | Likely benign (Oct 24, 2022) | |||
3-149872051-C-A | Uncertain significance (Jul 12, 2022) | |||
3-149872066-A-AGGC | Uncertain significance (Oct 13, 2022) | |||
3-149872071-A-G | Uncertain significance (Feb 14, 2022) | |||
3-149872086-G-A | Uncertain significance (Sep 24, 2021) | |||
3-149872095-A-T | Developmental and epileptic encephalopathy, 73 | Uncertain significance (May 06, 2021) | ||
3-149872100-A-G | Likely benign (Aug 16, 2022) | |||
3-149872107-A-T | Inborn genetic diseases | Uncertain significance (Jan 10, 2023) | ||
3-149872115-C-T | Likely benign (Aug 01, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RNF13 | protein_coding | protein_coding | ENST00000344229 | 9 | 149432 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000403 | 0.963 | 125732 | 0 | 12 | 125744 | 0.0000477 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.901 | 158 | 193 | 0.818 | 0.00000919 | 2506 |
Missense in Polyphen | 39 | 57.7 | 0.67591 | 788 | ||
Synonymous | -0.618 | 77 | 70.4 | 1.09 | 0.00000353 | 705 |
Loss of Function | 1.86 | 8 | 16.0 | 0.499 | 6.69e-7 | 244 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000120 | 0.000120 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000546 | 0.0000527 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.0000677 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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