RILPL2

Rab interacting lysosomal protein like 2

Basic information

Region (hg38): 12:123409714-123436684

Links

ENSG00000150977 ∙ NCBI:196383 ∙ OMIM:614093 ∙ HGNC:28787 ∙ Uniprot:Q969X0 ∙ 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 RILPL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RILPL2 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				1		1
missense			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in RILPL2

This is a list of pathogenic ClinVar variants found in the RILPL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-123415907-G-A		not specified	Uncertain significance (Feb 16, 2023)
12-123415908-A-G		not specified	Uncertain significance (Sep 28, 2022)
12-123423083-G-C		not specified	Uncertain significance (Mar 29, 2023)
12-123423084-C-T		not specified	Uncertain significance (Dec 21, 2023)
12-123423147-G-C		not specified	Uncertain significance (May 31, 2022)
12-123430542-G-C		not specified	Uncertain significance (Jul 12, 2023)
12-123430568-T-C		not specified	Uncertain significance (Oct 25, 2024)
12-123430622-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-123430634-A-G		not specified	Uncertain significance (Aug 14, 2023)
12-123430644-T-C		not specified	Likely benign (Oct 06, 2021)
12-123436095-G-A		not specified	Uncertain significance (Jun 22, 2021)
12-123436234-G-C		not specified	Uncertain significance (Oct 05, 2023)
12-123436246-G-A		not specified	Uncertain significance (Jul 10, 2024)
12-123436300-C-A		not specified	Uncertain significance (Nov 28, 2023)
12-123436340-C-G			Likely benign (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RILPL2	protein_coding	protein_coding	ENST00000280571	4	21329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00389	0.865	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.518	98	114	0.863	0.00000551	1340
Missense in Polyphen		32	38.093	0.84005		469
Synonymous	-0.308	52	49.2	1.06	0.00000242	417
Loss of Function	1.27	5	9.15	0.547	4.73e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000660	0.0000660
Ashkenazi Jewish	0.00	0.00
East Asian	0.000337	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000551	0.0000527
Middle Eastern	0.000337	0.000326
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in cell shape and neuronal morphogenesis, positively regulating the establishment and maintenance of dendritic spines. Plays a role in cellular protein transport, including protein transport away from primary cilia. May function via activation of RAC1 and PAK1 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0747

Intolerance Scores

• loftool: 0.136
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.0768
• hipred: N
• hipred_score: 0.244
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.699

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rilpl2

Gene ontology

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