RILPL1

protein-coding

Rab interacting lysosomal protein like 1

Gene summary

Predicted to enable dynein light intermediate chain binding activity and small GTPase binding activity. Predicted to be involved in several processes, including epithelial cell morphogenesis; nitric oxide mediated signal transduction; and protein transport from ciliary membrane to plasma membrane. Located in centrosome; ciliary basal body; and cytosol. Implicated in oculopharyngodistal myopathy 4. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_178314.5

Inheritance

ClinVar variants

U:51B:4

Top phenotype

Oculopharyngodistal myopathy 4

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr12:123,470,054-123,533,719

External References & Databases

Ensembl (ENSG00000188026)

Transcript & Mutation Effects

hg38 • Region Span ~63.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

oculopharyngodistal myopathy 4LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0030712

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Oculopharyngodistal myopathy 4AD

Manifestation: Musculoskeletal

Intervention: General

Rationale: 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

Refs: 35148830

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RILPL1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 47

Oculopharyngodistal myopathy 4Total: 3

RILPL1-related disorderTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178314.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	4 clinvar		5
missense			48 clinvar			48
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	4	0	55

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178314.5	RefSeq	NP_847884.2	7	MANE Select
ENST00000376874.9	Ensembl	ENSP00000366070.4	7	MANE Select
NM_001319243.2	RefSeq	NP_001306172.1	8	Standard
NM_001319244.2	RefSeq	NP_001306173.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

epithelial cell morphogenesis
cilium assembly
regulation of neuron death
protein transport from ciliary membrane to plasma membrane

Molecular Function

small GTPase binding
protein dimerization activity
dynein light intermediate chain binding

Cellular Component

nucleoplasm
cytoplasm
centrosome
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376874
Coding exons: 7
Length: 62341
Individuals with no LoFs: 124638
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 124665
p: 0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.13	152	246	0.618	0.0000145	2609
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0012	0.0011	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.000068	0.000065	rare
Other	0.00019	0.00017	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.323

Gene Damage Prediction

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