RILPL2

Rab interacting lysosomal protein like 2

Basic information

Region (hg38): 12:123409714-123436684

Links

ENSG00000150977NCBI:196383OMIM:614093HGNC:28787Uniprot:Q969X0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RILPL2 gene.

  • not_specified (27 variants)
  • not_provided (1 variants)

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. These statistics are base on transcript: NM_000145058.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
26
clinvar
1
clinvar
27
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 26 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RILPL2protein_codingprotein_codingENST00000280571 421329
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.003890.8651257320151257470.0000596
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.518981140.8630.000005511340
Missense in Polyphen3238.0930.84005469
Synonymous-0.3085249.21.060.00000242417
Loss of Function1.2759.150.5474.73e-7102

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006600.0000660
Ashkenazi Jewish0.000.00
East Asian0.0003370.000326
Finnish0.00004620.0000462
European (Non-Finnish)0.00005510.0000527
Middle Eastern0.0003370.000326
South Asian0.000.00
Other0.000.00

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
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.699

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rilpl2
Phenotype

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