RFT1

RFT1 homolog

Basic information

Region (hg38): 3:53088482-53130453

Links

ENSG00000163933 ∙ NCBI:91869 ∙ OMIM:611908 ∙ HGNC:30220 ∙ Uniprot:Q96AA3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• RFT1-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• RFT1-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• RFT1-congenital disorder of glycosylation (Strong), mode of inheritance: AR
• RFT1-congenital disorder of glycosylation (Supportive), mode of inheritance: AR
• RFT1-congenital disorder of glycosylation (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital disorder of glycosylation, type In	AR	Hematologic	Awareness of coagulopathies may be beneficial in terms of medical management, especially in situations such as surgery	Biochemical; Gastrointestinal; Hematologic; Neurologic	9516657; 10801058; 18313027; 19701946
Hepatic-metabolized agents should be avoided

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RFT1 gene.

• RFT1-congenital disorder of glycosylation (435 variants)
• not provided (67 variants)
• Inborn genetic diseases (24 variants)
• not specified (18 variants)
• Congenital disorder of glycosylation (3 variants)
• RFT1 related CDG (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFT1 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			4	76	1	81
missense	1	4	153	7	2	167
nonsense		1	5			6
start loss			1			1
frameshift		3	7			10
inframe indel			3			3
splice donor/acceptor (+/-2bp)			5			5
splice region			19	18		37
non coding			61	50	54	165
Total	1	8	239	133	57

Highest pathogenic variant AF is 0.0000131

Variants in RFT1

This is a list of pathogenic ClinVar variants found in the RFT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-53088555-T-C		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53088561-A-G		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
3-53088617-G-A		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53088712-T-C		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53088810-G-A		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
3-53088810-G-C		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53088835-T-G		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53088847-AAAG-A		Congenital disorder of glycosylation	Uncertain significance (Jun 14, 2016)
3-53088906-G-C		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53088907-C-T		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53088908-G-A		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
3-53088911-C-T		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53088912-G-A		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53088953-G-A		RFT1-congenital disorder of glycosylation	Benign (Jan 12, 2018)
3-53089016-C-T		RFT1-congenital disorder of glycosylation	Benign (Jan 12, 2018)
3-53089063-A-T		RFT1-congenital disorder of glycosylation	Benign (Jan 12, 2018)
3-53089083-C-T		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53089113-C-T		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
3-53089114-G-A		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53089116-C-G		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
3-53089197-G-A		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
3-53089248-A-G		RFT1-congenital disorder of glycosylation	Benign (Jan 13, 2018)
3-53089257-A-G		RFT1-congenital disorder of glycosylation	Benign (Jan 13, 2018)
3-53089446-T-C		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 12, 2018)
3-53089450-A-G		RFT1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFT1	protein_coding	protein_coding	ENST00000296292	13	41980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.74e-13	0.289	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.967	248	295	0.842	0.0000161	3431
Missense in Polyphen		98	111.24	0.88097		1355
Synonymous	0.330	119	124	0.962	0.00000670	1149
Loss of Function	1.15	23	29.8	0.772	0.00000162	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000388	0.000387
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000286	0.000281
Middle Eastern	0.0000546	0.0000544
South Asian	0.000262	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in N-linked oligosaccharide assembly. May participate in the translocation of oligosaccharide from the cytoplasmic side to the lumenal side of the endoplasmic reticulum membrane. {ECO:0000269|PubMed:18313027}.
• Disease: DISEASE: Congenital disorder of glycosylation 1N (CDG1N) [MIM:612015]: A form of congenital disorder of glycosylation, a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269|PubMed:18313027, ECO:0000269|PubMed:19701946}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Post-translational protein modification;Metabolism of proteins;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.227
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.57

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.154
• ghis: 0.516

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0453

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rft1

Gene ontology

• Biological process: carbohydrate transport;glycolipid translocation
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: lipid transporter activity