RIN1

Ras and Rab interactor 1, the group of VPS9 domain containing

Basic information

Region (hg38): 11:66330241-66336840

Links

ENSG00000174791NCBI:9610OMIM:605965HGNC:18749Uniprot:Q13671AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RIN1 gene.

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
3
clinvar
2
clinvar
5
missense
86
clinvar
5
clinvar
2
clinvar
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)2548652
11-66332292-C-T not specified Likely benign (Oct 30, 2024)3433480
11-66332355-C-A not specified Uncertain significance (May 18, 2023)2548808
11-66332380-C-G not specified Uncertain significance (Jul 26, 2024)3433481
11-66332383-G-A not specified Uncertain significance (Dec 05, 2024)2342183
11-66332417-C-T Benign (Dec 31, 2019)785361
11-66332466-T-A not specified Uncertain significance (Oct 22, 2021)2256520
11-66332521-G-A not specified Uncertain significance (Aug 02, 2021)2364568
11-66332530-C-T Benign (Dec 31, 2019)785362
11-66332558-G-A Benign (Dec 26, 2018)776629
11-66332566-C-A not specified Uncertain significance (Jun 07, 2024)3314376
11-66332571-G-A not specified Uncertain significance (Nov 09, 2023)3154408
11-66332577-A-G not specified Uncertain significance (Dec 11, 2023)3154407
11-66332581-G-A not specified Uncertain significance (Aug 02, 2021)3154406
11-66332599-T-C not specified Uncertain significance (Jul 30, 2023)2602031
11-66332699-G-C Benign/Likely benign (Jan 01, 2023)775092
11-66332715-C-G not specified Uncertain significance (Aug 02, 2022)2220927
11-66333268-T-C not specified Uncertain significance (Dec 27, 2023)3154405
11-66333283-C-T not specified Uncertain significance (Apr 04, 2023)2532750
11-66333310-C-T not specified Uncertain significance (Dec 26, 2023)3154404
11-66333355-C-T not specified Likely benign (Mar 07, 2024)3154403
11-66333361-C-T not specified Uncertain significance (Dec 05, 2022)2206456
11-66333614-C-T Benign (Dec 26, 2018)720437
11-66333641-C-T not specified Uncertain significance (Dec 27, 2023)3154402
11-66333647-C-T not specified Uncertain significance (Aug 23, 2021)2223450

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RIN1protein_codingprotein_codingENST00000311320 106599
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.51e-70.9411257110281257390.000111
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5534104430.9260.00002794808
Missense in Polyphen154176.060.87472032
Synonymous-1.262232001.110.00001191777
Loss of Function1.851423.70.5910.00000128275

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00003020.0000302
Ashkenazi Jewish0.00009960.0000992
East Asian0.0002180.000217
Finnish0.000.00
European (Non-Finnish)0.0001830.000167
Middle Eastern0.0002180.000217
South Asian0.00003270.0000327
Other0.0003280.000326

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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