ARK2C
arkadia (RNF111) C-terminal like ring finger ubiquitin ligase 2C, the group of Ring finger proteins
Basic information
Region (hg38): 18:46326809-46463140
Previous symbols: [ "RNF165" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 ARK2C 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 | 0 | |||||
| missense | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in ARK2C
This is a list of pathogenic ClinVar variants found in the ARK2C region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-46433265-A-C | not specified | Uncertain significance (Dec 03, 2021) | ||
| 18-46433322-G-C | not specified | Uncertain significance (Sep 03, 2024) | ||
| 18-46433351-A-C | not specified | Uncertain significance (May 01, 2022) | ||
| 18-46433468-C-A | not specified | Uncertain significance (Jun 10, 2024) | ||
| 18-46435311-G-C | not specified | Uncertain significance (Sep 20, 2023) | ||
| 18-46435323-C-T | not specified | Uncertain significance (Sep 26, 2023) | ||
| 18-46435352-A-C | not specified | Uncertain significance (Jan 31, 2024) | ||
| 18-46447571-G-C | not specified | Uncertain significance (Nov 10, 2022) | ||
| 18-46447597-C-G | not specified | Uncertain significance (Feb 26, 2024) | ||
| 18-46447617-C-G | not specified | Uncertain significance (Nov 27, 2023) | ||
| 18-46450312-G-A | not specified | Uncertain significance (Sep 08, 2024) | ||
| 18-46450341-C-G | not specified | Uncertain significance (Jul 14, 2021) | ||
| 18-46450383-G-A | not specified | Uncertain significance (Jun 07, 2023) | ||
| 18-46456628-G-A | not specified | Uncertain significance (Jul 13, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARK2C | protein_coding | protein_coding | ENST00000269439 | 8 | 136332 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.972 | 0.0281 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.94 | 134 | 214 | 0.627 | 0.0000129 | 2247 |
| Missense in Polyphen | 36 | 71.346 | 0.50459 | 780 | ||
| Synonymous | -0.131 | 91 | 89.4 | 1.02 | 0.00000566 | 687 |
| Loss of Function | 3.71 | 2 | 19.8 | 0.101 | 0.00000108 | 190 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000616 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase that acts as a regulator of motor axon elongation. Required for efficient motor axon extension in the dorsal forelimb by enhancing the transcriptional responses of the SMAD1/SMAD5/SMAD8 effectors, which are activated downstream of BMP. Acts by mediating ubiquitination and degradation of SMAD inhibitors such as SMAD6, SMAD7, SKI and SNON isoform of SKIL. {ECO:0000250|UniProtKB:E9QAU8}.;
Recessive Scores
- pRec
- 0.0880
Intolerance Scores
- loftool
- 0.0847
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.93
Haploinsufficiency Scores
- pHI
- 0.145
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.533
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rnf165
- Phenotype
- growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); limbs/digits/tail 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);
Gene ontology
- Biological process
- protein polyubiquitination;motor neuron axon guidance;multicellular organism aging;protein catabolic process;positive regulation of BMP signaling pathway;forelimb morphogenesis;innervation;muscle structure development
- Cellular component
- nucleus;protein-containing complex
- Molecular function
- protein binding;zinc ion binding;ubiquitin protein ligase activity