RILP

Rab interacting lysosomal protein

Basic information

Region (hg38): 17:1646145-1649866

Links

ENSG00000167705 ∙ NCBI:83547 ∙ OMIM:607848 ∙ HGNC:30266 ∙ Uniprot:Q96NA2 ∙ 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 RILP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RILP 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			36	2		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	0

Variants in RILP

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

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

Position	Type	Phenotype	Significance	ClinVar
17-1646461-G-A		not specified	Uncertain significance (May 30, 2024)
17-1646473-C-A		not specified	Uncertain significance (Jan 23, 2024)
17-1646482-T-A		not specified	Uncertain significance (Dec 21, 2024)
17-1646513-C-T		not specified	Likely benign (Jul 27, 2021)
17-1646528-G-C		not specified	Uncertain significance (Feb 22, 2023)
17-1646542-C-A		not specified	Uncertain significance (Jun 18, 2021)
17-1646554-C-A		not specified	Uncertain significance (Aug 02, 2021)
17-1646979-C-T		not specified	Uncertain significance (Jan 22, 2024)
17-1647887-G-A		not specified	Uncertain significance (Jan 09, 2024)
17-1647896-G-A		not specified	Uncertain significance (Dec 03, 2021)
17-1647950-G-A		not specified	Uncertain significance (Sep 16, 2021)
17-1648420-T-G		not specified	Uncertain significance (Feb 06, 2025)
17-1648468-G-C		not specified	Uncertain significance (Nov 10, 2022)
17-1648486-C-T		not specified	Uncertain significance (Dec 23, 2024)
17-1648815-C-T		not specified	Uncertain significance (Apr 28, 2022)
17-1648819-G-T		not specified	Uncertain significance (Jun 09, 2022)
17-1648841-C-A		not specified	Uncertain significance (Sep 27, 2024)
17-1648870-C-T		not specified	Uncertain significance (Oct 16, 2024)
17-1648890-C-T		not specified	Uncertain significance (Nov 17, 2023)
17-1648920-G-A		not specified	Uncertain significance (Nov 09, 2023)
17-1648921-C-T		not specified	Uncertain significance (Aug 07, 2024)
17-1648931-C-G		not specified	Uncertain significance (Aug 15, 2023)
17-1648971-T-A		not specified	Uncertain significance (Jan 09, 2024)
17-1649201-G-T		not specified	Uncertain significance (Jun 25, 2024)
17-1649211-C-T		not specified	Uncertain significance (Jun 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RILP	protein_coding	protein_coding	ENST00000301336	8	3928

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.34e-11	0.0285	125714	0	24	125738	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0185	197	196	1.00	0.0000102	2467
Missense in Polyphen		63	76.595	0.82251		1047
Synonymous	-0.0958	90	88.9	1.01	0.00000463	849
Loss of Function	-0.404	15	13.4	1.12	5.76e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000209	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000118	0.000114
Middle Eastern	0.000114	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rab effector playing a role in late endocytic transport to degradative compartments. Involved in the regulation of lysosomal morphology and distribution. Induces recruitment of dynein-dynactin motor complexes to Rab7A-containing late endosome and lysosome compartments. Promotes centripetal migration of phagosomes and the fusion of phagosomes with the late endosomes and lysosomes. {ECO:0000269|PubMed:11179213, ECO:0000269|PubMed:11696325, ECO:0000269|PubMed:12944476, ECO:0000269|PubMed:14668488}.
• Pathway: Salmonella infection - Homo sapiens (human);Phagosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0897

Haploinsufficiency Scores

• pHI: 0.0921
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.523

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rilp

Gene ontology

• Biological process: endosome to lysosome transport;regulation of multivesicular body size;protein transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;endosome transport via multivesicular body sorting pathway;negative regulation of protein catabolic process;early endosome to late endosome transport;positive regulation of protein catabolic process;cilium assembly;intralumenal vesicle formation
• Cellular component: cytoplasm;lysosome;lysosomal membrane;late endosome;cytosol;phagocytic vesicle membrane;late endosome membrane;protein-containing complex;ciliary basal body
• Molecular function: protein binding;Rab GTPase binding;small GTPase binding;protein dimerization activity;dynein light intermediate chain binding