RIN1
Basic information
Region (hg38): 11:66330241-66336840
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 RIN1 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 | 5 | |||||
missense | 86 | 93 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 86 | 8 | 4 |
Variants in RIN1
This is a list of pathogenic ClinVar variants found in the RIN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-66332290-C-T | not specified | Uncertain significance (May 18, 2023) | ||
11-66332292-C-T | not specified | Likely benign (Oct 30, 2024) | ||
11-66332355-C-A | not specified | Uncertain significance (May 18, 2023) | ||
11-66332380-C-G | not specified | Uncertain significance (Jul 26, 2024) | ||
11-66332383-G-A | not specified | Uncertain significance (Dec 05, 2024) | ||
11-66332417-C-T | Benign (Dec 31, 2019) | |||
11-66332466-T-A | not specified | Uncertain significance (Oct 22, 2021) | ||
11-66332521-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
11-66332530-C-T | Benign (Dec 31, 2019) | |||
11-66332558-G-A | Benign (Dec 26, 2018) | |||
11-66332566-C-A | not specified | Uncertain significance (Jun 07, 2024) | ||
11-66332571-G-A | not specified | Uncertain significance (Nov 09, 2023) | ||
11-66332577-A-G | not specified | Uncertain significance (Dec 11, 2023) | ||
11-66332581-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
11-66332599-T-C | not specified | Uncertain significance (Jul 30, 2023) | ||
11-66332699-G-C | Benign/Likely benign (Jan 01, 2023) | |||
11-66332715-C-G | not specified | Uncertain significance (Aug 02, 2022) | ||
11-66333268-T-C | not specified | Uncertain significance (Dec 27, 2023) | ||
11-66333283-C-T | not specified | Uncertain significance (Apr 04, 2023) | ||
11-66333310-C-T | not specified | Uncertain significance (Dec 26, 2023) | ||
11-66333355-C-T | not specified | Likely benign (Mar 07, 2024) | ||
11-66333361-C-T | not specified | Uncertain significance (Dec 05, 2022) | ||
11-66333614-C-T | Benign (Dec 26, 2018) | |||
11-66333641-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
11-66333647-C-T | not specified | Uncertain significance (Aug 23, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RIN1 | protein_coding | protein_coding | ENST00000311320 | 10 | 6599 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.51e-7 | 0.941 | 125711 | 0 | 28 | 125739 | 0.000111 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.553 | 410 | 443 | 0.926 | 0.0000279 | 4808 |
Missense in Polyphen | 154 | 176.06 | 0.8747 | 2032 | ||
Synonymous | -1.26 | 223 | 200 | 1.11 | 0.0000119 | 1777 |
Loss of Function | 1.85 | 14 | 23.7 | 0.591 | 0.00000128 | 275 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000302 | 0.0000302 |
Ashkenazi Jewish | 0.0000996 | 0.0000992 |
East Asian | 0.000218 | 0.000217 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000183 | 0.000167 |
Middle Eastern | 0.000218 | 0.000217 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.000328 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Ras effector protein, which may serve as an inhibitory modulator of neuronal plasticity in aversive memory formation. Can affect Ras signaling at different levels. First, by competing with RAF1 protein for binding to activated Ras. Second, by enhancing signaling from ABL1 and ABL2, which regulate cytoskeletal remodeling. Third, by activating RAB5A, possibly by functioning as a guanine nucleotide exchange factor (GEF) for RAB5A, by exchanging bound GDP for free GTP, and facilitating Ras-activated receptor endocytosis. {ECO:0000269|PubMed:15886098, ECO:0000269|PubMed:9144171, ECO:0000269|PubMed:9208849}.;
- Pathway
- Ras signaling pathway - Homo sapiens (human);Ras Signaling;EGF-EGFR Signaling Pathway;Regulation of Ras family activation;Vesicle-mediated transport;Membrane Trafficking;EGFR1;ErbB1 downstream signaling;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs
(Consensus)
Recessive Scores
- pRec
- 0.141
Intolerance Scores
- loftool
- 0.734
- rvis_EVS
- 0.27
- rvis_percentile_EVS
- 70.69
Haploinsufficiency Scores
- pHI
- 0.0771
- hipred
- N
- hipred_score
- 0.489
- ghis
- 0.553
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.909
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rin1
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- endocytosis;signal transduction;memory;associative learning;negative regulation of synaptic plasticity;positive regulation of GTPase activity
- Cellular component
- cytoplasm;cytosol;cytoskeleton;plasma membrane;dendrite;neuronal cell body
- Molecular function
- GTPase activator activity;protein binding;Rab guanyl-nucleotide exchange factor activity