RIN1

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

Basic information

Region (hg38): 11:66330241-66336840

Links

ENSG00000174791 ∙ NCBI:9610 ∙ OMIM:605965 ∙ HGNC:18749 ∙ Uniprot:Q13671 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	2	5
missense			86	5	2	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: gnomAD

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: 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

	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