RNF10
Basic information
Region (hg38): 12:120533479-120577588
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF10 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 | |||||
missense | 45 | 47 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 45 | 2 | 1 |
Variants in RNF10
This is a list of pathogenic ClinVar variants found in the RNF10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-120534842-A-G | not specified | Uncertain significance (Mar 07, 2024) | ||
12-120534864-A-G | not specified | Uncertain significance (Dec 22, 2023) | ||
12-120534868-C-A | not specified | Uncertain significance (Nov 23, 2022) | ||
12-120534870-G-C | not specified | Uncertain significance (Apr 15, 2024) | ||
12-120534876-A-G | not specified | Likely benign (Apr 07, 2023) | ||
12-120534893-T-A | not specified | Uncertain significance (Jun 29, 2023) | ||
12-120534953-T-G | not specified | Uncertain significance (Jan 10, 2022) | ||
12-120546431-C-T | not specified | Uncertain significance (Mar 15, 2024) | ||
12-120546432-G-A | not specified | Uncertain significance (Oct 18, 2021) | ||
12-120546441-G-A | not specified | Uncertain significance (Jun 02, 2023) | ||
12-120546468-A-G | not specified | Uncertain significance (Dec 11, 2023) | ||
12-120546494-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
12-120546534-C-T | not specified | Uncertain significance (Sep 23, 2023) | ||
12-120546539-C-G | not specified | Uncertain significance (Nov 09, 2023) | ||
12-120546551-G-A | not specified | Uncertain significance (Jul 13, 2021) | ||
12-120546580-T-C | Likely benign (Jul 16, 2018) | |||
12-120552532-G-A | not specified | Uncertain significance (Oct 24, 2023) | ||
12-120552557-T-A | not specified | Uncertain significance (Jun 16, 2023) | ||
12-120552605-C-T | not specified | Uncertain significance (Jun 21, 2023) | ||
12-120554723-A-G | not specified | Uncertain significance (Nov 27, 2023) | ||
12-120557315-A-G | not specified | Uncertain significance (May 23, 2023) | ||
12-120557328-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
12-120557565-C-T | not specified | Uncertain significance (Nov 09, 2021) | ||
12-120557593-C-T | not specified | Uncertain significance (Jan 26, 2023) | ||
12-120557599-A-G | not specified | Uncertain significance (Jan 03, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RNF10 | protein_coding | protein_coding | ENST00000325954 | 17 | 44115 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.164 | 0.836 | 125596 | 0 | 152 | 125748 | 0.000605 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.777 | 416 | 463 | 0.898 | 0.0000255 | 5326 |
Missense in Polyphen | 78 | 121.7 | 0.64095 | 1354 | ||
Synonymous | 0.470 | 163 | 171 | 0.954 | 0.00000906 | 1573 |
Loss of Function | 4.51 | 10 | 41.3 | 0.242 | 0.00000200 | 495 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000632 | 0.000570 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000168 | 0.000163 |
Finnish | 0.000253 | 0.000231 |
European (Non-Finnish) | 0.00114 | 0.00113 |
Middle Eastern | 0.000168 | 0.000163 |
South Asian | 0.0000654 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional factor involved in the regulation of MAG (Myelin-associated glycoprotein) expression. Acts as a regulator of Schwann cell differentiation and myelination. {ECO:0000250|UniProtKB:Q5XI59}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.150
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 18.14
Haploinsufficiency Scores
- pHI
- 0.309
- hipred
- N
- hipred_score
- 0.426
- ghis
- 0.522
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.963
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rnf10
- Phenotype
- immune system phenotype; skeleton phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype; 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); 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); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; muscle phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Gene ontology
- Biological process
- negative regulation of Schwann cell proliferation;positive regulation of myelination;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;protein autoubiquitination
- Cellular component
- nucleus;cytoplasm
- Molecular function
- ubiquitin-protein transferase activity;protein binding;transcription regulatory region DNA binding;metal ion binding