RINL

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

Basic information

Region (hg38): 19:38867829-38878275

Links

ENSG00000187994 ∙ NCBI:126432 ∙ ∙ HGNC:24795 ∙ Uniprot:Q6ZS11 ∙ 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 RINL gene.

• Inborn genetic diseases (26 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RINL 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				2		2
missense			24	2		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	24	4	1

Variants in RINL

This is a list of pathogenic ClinVar variants found in the RINL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-38869142-A-G		not specified	Uncertain significance (Apr 06, 2023)
19-38869641-A-G		not specified	Uncertain significance (Oct 04, 2022)
19-38869666-C-G		not specified	Uncertain significance (Jul 22, 2022)
19-38869958-G-C			Uncertain significance (Jan 01, 2024)
19-38870060-G-C		not specified	Uncertain significance (Jul 12, 2022)
19-38870121-C-T			Likely benign (May 01, 2022)
19-38870129-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-38870134-C-T		not specified	Uncertain significance (Jan 05, 2022)
19-38870173-G-A		not specified	Uncertain significance (Oct 10, 2023)
19-38870174-G-T		not specified	Uncertain significance (Oct 05, 2021)
19-38870207-C-T		not specified	Uncertain significance (Dec 15, 2022)
19-38870234-G-T		not specified	Uncertain significance (May 17, 2023)
19-38870662-G-A		not specified	Likely benign (Dec 27, 2022)
19-38870713-C-T		not specified	Uncertain significance (May 17, 2023)
19-38870774-C-T		not specified	Uncertain significance (Jun 11, 2021)
19-38870828-C-G		not specified	Uncertain significance (Jul 06, 2021)
19-38870849-C-T		not specified	Uncertain significance (Dec 21, 2023)
19-38870947-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-38870969-C-A		not specified	Uncertain significance (Jul 14, 2021)
19-38871086-T-C		not specified	Uncertain significance (Oct 03, 2022)
19-38871120-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-38871153-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-38871637-C-T			Benign (Jan 30, 2018)
19-38871683-G-A		not specified	Uncertain significance (Jan 09, 2024)
19-38871689-G-A		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RINL	protein_coding	protein_coding	ENST00000591812	11	10450

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000520	0.994	125715	0	26	125741	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	251	312	0.804	0.0000170	3555
Missense in Polyphen		63	94.785	0.66466		1106
Synonymous	2.42	102	138	0.738	0.00000808	1231
Loss of Function	2.42	11	23.7	0.464	0.00000111	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000319	0.000319
Ashkenazi Jewish	0.00	0.00
East Asian	0.000116	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000748	0.0000703
Middle Eastern	0.000116	0.000109
South Asian	0.000167	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) for RAB5A and RAB22A that activates RAB5A and RAB22A by exchanging bound GDP for free GTP. Plays a role in endocytosis via its role in activating Rab family members (By similarity). {ECO:0000250}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Intolerance Scores

• loftool: 0.727
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.281
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.388

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rinl

Gene ontology

• Biological process: endocytosis;protein transport;positive regulation of GTPase activity
• Cellular component: ruffle;actin cytoskeleton;cytoplasmic vesicle
• Molecular function: guanyl-nucleotide exchange factor activity;GTPase activator activity