RFTN1

raftlin, lipid raft linker 1

Basic information

Region (hg38): 3:16313573-16514026

Links

ENSG00000131378 ∙ NCBI:23180 ∙ OMIM:618210 ∙ HGNC:30278 ∙ Uniprot:Q14699 ∙ 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 RFTN1 gene.

• Inborn genetic diseases (24 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFTN1 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				3		3
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	4	0

Variants in RFTN1

This is a list of pathogenic ClinVar variants found in the RFTN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-16316835-T-C		not specified	Uncertain significance (Aug 18, 2021)
3-16316844-G-A		not specified	Uncertain significance (Nov 09, 2021)
3-16316999-A-G			Likely benign (Mar 01, 2023)
3-16317041-C-T		not specified	Uncertain significance (May 03, 2023)
3-16317048-T-C		not specified	Uncertain significance (Jan 05, 2022)
3-16317106-T-C		not specified	Uncertain significance (Jul 05, 2023)
3-16317108-G-T		not specified	Uncertain significance (Aug 18, 2021)
3-16317130-T-C		not specified	Uncertain significance (Jan 25, 2023)
3-16317175-C-T		not specified	Uncertain significance (May 30, 2023)
3-16317210-T-C		not specified	Uncertain significance (Nov 07, 2022)
3-16317213-C-T		not specified	Uncertain significance (Jun 13, 2023)
3-16326790-G-A			Likely benign (Mar 01, 2023)
3-16370103-C-T		not specified	Uncertain significance (Aug 21, 2023)
3-16370160-C-T		not specified	Uncertain significance (Mar 02, 2023)
3-16370169-C-T		not specified	Likely benign (Aug 02, 2021)
3-16370228-C-A		not specified	Uncertain significance (Jun 11, 2021)
3-16370229-G-A		not specified	Uncertain significance (Sep 22, 2023)
3-16377752-G-T		not specified	Uncertain significance (May 31, 2023)
3-16377756-C-T		not specified	Uncertain significance (Dec 13, 2021)
3-16377808-C-G		not specified	Uncertain significance (Oct 22, 2021)
3-16377820-C-T		not specified	Uncertain significance (Dec 01, 2022)
3-16377832-T-G		not specified	Uncertain significance (Jun 24, 2022)
3-16377845-G-A			Likely benign (Dec 01, 2022)
3-16377850-G-C		not specified	Uncertain significance (Nov 12, 2021)
3-16377952-C-T		not specified	Uncertain significance (Oct 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFTN1	protein_coding	protein_coding	ENST00000334133	9	200453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000242	0.916	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.395	312	332	0.939	0.0000190	3761
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000212	0.000211
Ashkenazi Jewish	0.000414	0.000397
East Asian	0.000163	0.000163
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.000164	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.146
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rftn1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: membrane raft assembly;T cell antigen processing and presentation;protein transport into membrane raft;interleukin-17 production;dsRNA transport;toll-like receptor 3 signaling pathway;positive regulation of growth rate;response to exogenous dsRNA;T cell receptor signaling pathway;B cell receptor signaling pathway;protein localization to membrane raft
• Cellular component: cytoplasm;endosome;early endosome;plasma membrane;protein-containing complex;membrane raft;extracellular exosome
• Molecular function: double-stranded RNA binding