RFNG

RFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase, the group of Beta 3-glycosyltransferases

Basic information

Region (hg38): 17:82047901-82051831

Links

ENSG00000169733 ∙ NCBI:5986 ∙ OMIM:602578 ∙ HGNC:9974 ∙ Uniprot:Q9Y644 ∙ 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 RFNG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFNG 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				2	1	3
missense			21	4		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	21	6	1

Variants in RFNG

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

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

Position	Type	Phenotype	Significance	ClinVar
17-82048736-G-A		not specified	Likely benign (May 18, 2023)
17-82048739-G-A		not specified	Likely benign (Sep 16, 2021)
17-82048745-C-T		not specified	Uncertain significance (Aug 13, 2021)
17-82049032-G-A		not specified	Uncertain significance (Aug 20, 2023)
17-82049077-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-82049086-G-C		not specified	Uncertain significance (Jul 26, 2021)
17-82049705-C-T		not specified	Uncertain significance (Feb 17, 2023)
17-82049739-G-A		not specified	Likely benign (Jun 27, 2023)
17-82049775-C-T		not specified	Uncertain significance (Dec 26, 2023)
17-82049807-C-T		not specified	Uncertain significance (May 13, 2022)
17-82049808-G-A		not specified	Uncertain significance (Oct 25, 2022)
17-82049846-G-C			Likely benign (Sep 01, 2022)
17-82049948-C-A		not specified	Uncertain significance (Jan 30, 2024)
17-82050000-T-C		not specified	Uncertain significance (Mar 07, 2024)
17-82050403-G-A		not specified	Uncertain significance (Dec 19, 2023)
17-82050453-G-A			Likely benign (Sep 01, 2022)
17-82050481-G-C		not specified	Uncertain significance (Sep 29, 2023)
17-82050503-G-A		not specified	Uncertain significance (Dec 20, 2023)
17-82050511-C-T		not specified	Uncertain significance (Oct 06, 2021)
17-82050518-C-A		not specified	Uncertain significance (Feb 22, 2023)
17-82050518-C-T		not specified	Uncertain significance (Dec 19, 2022)
17-82050666-G-A		not specified	Uncertain significance (May 31, 2022)
17-82050705-T-C		not specified	Uncertain significance (Dec 03, 2021)
17-82050728-C-T		not specified	Likely benign (Jan 03, 2024)
17-82051552-C-G		not specified	Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFNG	protein_coding	protein_coding	ENST00000310496	8	3930

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.79e-9	0.0549	125466	0	27	125493	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.234	152	160	0.948	0.00000994	2090
Missense in Polyphen		80	91.239	0.87682		1006
Synonymous	-3.49	103	66.8	1.54	0.00000440	694
Loss of Function	-0.468	12	10.4	1.16	4.42e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000120
Ashkenazi Jewish	0.0000997	0.0000995
East Asian	0.000218	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.0000920	0.0000882
Middle Eastern	0.000218	0.000218
South Asian	0.000308	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycosyltransferase that initiates the elongation of O- linked fucose residues attached to EGF-like repeats in the extracellular domain of Notch molecules. Modulates NOTCH1 activity by modifying O-fucose residues at specific EGF-like domains resulting in enhancement of NOTCH1 activation by DLL1 and JAG1. May be involved in limb formation and in neurogenesis. {ECO:0000250|UniProtKB:O09009, ECO:0000250|UniProtKB:O12972, ECO:0000250|UniProtKB:Q9R1U9}.
• Pathway: Other types of O-glycan biosynthesis - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Notch Signaling Pathway;Notch Signaling Pathway;Signal Transduction;Notch;Pre-NOTCH Processing in Golgi;Pre-NOTCH Expression and Processing;Signaling by NOTCH (Consensus)

Recessive Scores

• pRec: 0.120

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.301
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.448

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rfng
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; skeleton phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype

Zebrafish Information Network

• Gene name: rfng
• Affected structure: fourth ventricle
• Phenotype tag: abnormal
• Phenotype quality: structure

Gene ontology

• Biological process: pattern specification process;nervous system development;regulation of Notch signaling pathway;animal organ morphogenesis;cell differentiation;positive regulation of protein binding;protein O-linked fucosylation;positive regulation of Notch signaling pathway
• Cellular component: extracellular region;integral component of Golgi membrane
• Molecular function: molecular_function;acetylglucosaminyltransferase activity;O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity;metal ion binding