RFTN1

protein-coding

raftlin, lipid raft linker 1

Gene summary

Enables double-stranded RNA binding activity. Involved in B cell receptor signaling pathway; membrane raft assembly; and positive regulation of growth rate. Acts upstream of or within dsRNA transport; response to exogenous dsRNA; and toll-like receptor 3 signaling pathway. Located in endosome; membrane raft; and plasma membrane. Part of protein-containing complex. Biomarker of glaucoma. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015150.2

Inheritance

—

ClinVar variants

U:78B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr3:16,313,574-16,514,026

External References & Databases

Ensembl (ENSG00000131378)

Transcript & Mutation Effects

hg38 • Region Span ~200.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RFTN1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015150.2. 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	3 clinvar		4
missense			75 clinvar	6 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	78	9	0	87

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015150.2	RefSeq	NP_055965.1	9	MANE Select
ENST00000334133.9	Ensembl	ENSP00000334153.4	9	MANE Select
ENST00000431547.1	Ensembl	ENSP00000393216.1	3	Standard
ENST00000432519.5	Ensembl	ENSP00000403926.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

membrane raft assembly
T cell antigen processing and presentation
protein transport into membrane raft
interleukin-17 production
dsRNA transport

Molecular Function

double-stranded RNA binding

Cellular Component

cytoplasm
endosome
early endosome
plasma membrane
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334133
Coding exons: 9
Length: 200453
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 36
Defined: 125748
p: 0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.395	312	332	0.939	0.0000190	3761
Missense (PolyPhen)		85	112.24	0.7573		1395
Synonymous	0.106	138	140	0.989	0.00000895	1140
Loss of Function	1.68	12	20.1	0.596	8.52e-7	253

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0.00041	0.00040	rare
East Asian	0.00016	0.00016	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00016	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in protein trafficking via association with clathrin and AP2 complex (PubMed:27022195, PubMed:21266579). Upon bacterial lipopolysaccharide stimulation, mediates internalization of TLR4 to endosomes in dendritic cells and macrophages; and internalization of poly(I:C) to TLR3-positive endosomes in myeloid dendritic cells and epithelial cells; resulting in activation of TICAM1-mediated signaling and subsequent IFNB1 production (PubMed:27022195, PubMed:21266579). Involved in T-cell antigen receptor-mediated signaling by regulating tyrosine kinase LCK localization, T-cell dependent antibody production and cytokine secretion (By similarity). May regulate B-cell antigen receptor- mediated signaling (PubMed:12805216). May play a pivotal role in the formation and/or maintenance of lipid rafts (PubMed:12805216). {ECO:0000250|UniProtKB:Q6A0D4, ECO:0000269|PubMed:12805216, ECO:0000269|PubMed:21266579, ECO:0000269|PubMed:27022195}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.882
RVIS EVS: -0.64
RVIS percentile EVS: 16.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.935

Gene Damage Prediction

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