RILPL1

Rab interacting lysosomal protein like 1

Basic information

Region (hg38): 12:123470054-123533719

Links

ENSG00000188026 ∙ NCBI:353116 ∙ OMIM:614092 ∙ HGNC:26814 ∙ Uniprot:Q5EBL4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• oculopharyngodistal myopathy 4 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Oculopharyngodistal myopathy 4	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	35148830

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RILPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RILPL1 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			16			16
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	17	0	0

Variants in RILPL1

This is a list of pathogenic ClinVar variants found in the RILPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-123472587-C-T		not specified	Uncertain significance (Sep 20, 2023)
12-123472618-C-T		not specified	Uncertain significance (Jan 06, 2023)
12-123472665-C-T		not specified	Uncertain significance (Jun 24, 2022)
12-123472672-A-G		not specified	Uncertain significance (May 31, 2022)
12-123475701-CATCT-C			Uncertain significance (May 01, 2023)
12-123485708-C-T		not specified	Uncertain significance (Sep 22, 2023)
12-123485738-T-C		not specified	Uncertain significance (Sep 27, 2022)
12-123485751-G-A		RILPL1-related disorder	Uncertain significance (Apr 06, 2023)
12-123485775-C-T		not specified	Uncertain significance (Nov 17, 2023)
12-123485783-C-G		not specified	Uncertain significance (Dec 07, 2021)
12-123485798-G-A		not specified	Uncertain significance (Sep 21, 2023)
12-123499447-G-T		not specified	Uncertain significance (Jun 29, 2022)
12-123523585-C-T		not specified	Uncertain significance (Dec 03, 2021)
12-123523624-C-G		Oculopharyngodistal myopathy 4	Uncertain significance (Mar 08, 2024)
12-123533203-G-A		not specified	Uncertain significance (Mar 07, 2024)
12-123533348-G-C		not specified	Uncertain significance (Oct 06, 2021)
12-123533434-TCTCCAGCGCCGACTCGGC-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
12-123533452-C-T		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RILPL1	protein_coding	protein_coding	ENST00000376874	7	62341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.386	0.614	124638	0	27	124665	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	152	246	0.618	0.0000145	2609
Missense in Polyphen		34	95.232	0.35702		994
Synonymous	1.27	91	108	0.844	0.00000669	762
Loss of Function	3.40	5	22.4	0.224	0.00000147	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00125	0.00106
Finnish	0.00	0.00
European (Non-Finnish)	0.0000354	0.0000354
Middle Eastern	0.00125	0.00106
South Asian	0.0000685	0.0000654
Other	0.000187	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of cell shape and polarity. Plays a role in cellular protein transport, including protein transport away from primary cilia. Neuroprotective protein, which acts by sequestring GAPDH in the cytosol and prevent the apoptotic function of GAPDH in the nucleus. Competes with SIAH1 for binding GAPDH (By similarity). Does not regulate lysosomal morphology and distribution. {ECO:0000250}.

Intolerance Scores

• loftool: 0.806
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.135
• hipred: Y
• hipred_score: 0.685
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.323

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rilpl1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: epithelial cell morphogenesis;cilium assembly;regulation of neuron death;protein transport from ciliary membrane to plasma membrane
• Cellular component: nucleoplasm;cytoplasm;centrosome;cytosol;plasma membrane;cilium;ciliary basal body
• Molecular function: small GTPase binding;protein dimerization activity;dynein light intermediate chain binding