RFTN2

raftlin family member 2

Basic information

Region (hg38): 2:197568224-197676045

Previous symbols: [ "C2orf11" ]

Links

ENSG00000162944 ∙ NCBI:130132 ∙ OMIM:618215 ∙ HGNC:26402 ∙ Uniprot:Q52LD8 ∙ 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 RFTN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFTN2 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						0
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in RFTN2

This is a list of pathogenic ClinVar variants found in the RFTN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-197572024-T-C		not specified	Uncertain significance (Jun 19, 2024)
2-197572033-C-G		not specified	Uncertain significance (Jul 29, 2023)
2-197572055-C-T		not specified	Uncertain significance (May 29, 2024)
2-197572076-C-T		not specified	Uncertain significance (Dec 13, 2023)
2-197572105-C-A		not specified	Uncertain significance (Jan 03, 2022)
2-197572107-G-C		not specified	Uncertain significance (Aug 13, 2021)
2-197572112-G-A		not specified	Likely benign (Jan 23, 2024)
2-197572162-C-T		not specified	Uncertain significance (Feb 13, 2024)
2-197572163-G-A		not specified	Uncertain significance (Mar 15, 2024)
2-197572202-A-G		not specified	Uncertain significance (Jun 13, 2024)
2-197572210-G-A		not specified	Uncertain significance (Jan 25, 2023)
2-197572231-C-T		not specified	Uncertain significance (Sep 01, 2021)
2-197572265-G-A		not specified	Uncertain significance (Feb 02, 2024)
2-197572268-G-A		not specified	Uncertain significance (Jul 30, 2023)
2-197596018-C-T		not specified	Uncertain significance (Nov 09, 2022)
2-197596041-C-T		not specified	Uncertain significance (Jun 02, 2023)
2-197615885-C-G		not specified	Uncertain significance (Oct 03, 2023)
2-197615901-G-C		not specified	Uncertain significance (Jan 06, 2023)
2-197617826-C-T		not specified	Uncertain significance (May 13, 2024)
2-197617849-C-T		not specified	Uncertain significance (Jun 18, 2024)
2-197617916-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-197633742-A-G		not specified	Uncertain significance (Oct 02, 2023)
2-197633787-G-T		not specified	Uncertain significance (May 18, 2023)
2-197633800-C-G		not specified	Uncertain significance (Sep 16, 2021)
2-197633886-G-C		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFTN2	protein_coding	protein_coding	ENST00000295049	9	107822

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000792	0.982	125713	0	34	125747	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.329	256	271	0.944	0.0000143	3261
Missense in Polyphen		67	92.73	0.72253		1174
Synonymous	2.28	74	103	0.715	0.00000606	953
Loss of Function	2.14	12	23.1	0.519	0.00000106	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000538	0.000536
Ashkenazi Jewish	0.00	0.00
East Asian	0.000497	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.000497	0.000489
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Upon bacterial lipopolysaccharide stimulation, mediates clathrin-dependent internalization of TLR4 in dendritic cells, resulting in activation of TICAM1-mediated signaling and subsequent IFNB1 production. May regulate B-cell antigen receptor- mediated signaling. {ECO:0000250|UniProtKB:Q8CHX7}.

Recessive Scores

• pRec: 0.0962

Intolerance Scores

• loftool: 0.869
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.16

Haploinsufficiency Scores

• pHI: 0.219
• hipred: N
• hipred_score: 0.256
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rftn2

Gene ontology

• Biological process: dsRNA transport;response to exogenous dsRNA
• Cellular component: plasma membrane