RFNG

protein-coding

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

Gene summary

Predicted to enable O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity. Predicted to be involved in regulation of Notch signaling pathway. Predicted to act upstream of or within positive regulation of Notch signaling pathway. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_002917.2

Inheritance

—

ClinVar variants

U:67B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.16

Max pathogenic AF

—

Genomic locus

chr17:82,047,902-82,051,831

External References & Databases

Ensembl (ENSG00000169733)

Transcript & Mutation Effects

hg38 • Region Span ~3.9 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 RFNG variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 71

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002917.2. 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				2 clinvar	1 clinvar	3
missense			65 clinvar	6 clinvar		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	67	8	1	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002917.2	RefSeq	NP_002908.1	8	MANE Select
ENST00000310496.9	Ensembl	ENSP00000307971.4	8	MANE Select
ENST00000429557.7	Ensembl	ENSP00000402931.3	6	Standard
ENST00000429557.8	Ensembl	ENSP00000402931.3	6	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rfng	Danio rerio	Structure: fourth ventricle Quality: structure abnormal

Gene / Model

Organism

Observed Phenotype

rfng

Danio rerio

Structure: fourth ventricle

Quality: structure

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

pattern specification process
nervous system development
regulation of Notch signaling pathway
animal organ morphogenesis
cell differentiation

Molecular Function

molecular_function
acetylglucosaminyltransferase activity
O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity
metal ion binding

Cellular Component

extracellular region
integral component of Golgi membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310496
Coding exons: 8
Length: 3930
Individuals with no LoFs: 125466
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125493
p: 0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.234	152	160	0.948	0.00000994	2090
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000092	0.000088	rare
South Asian	0.00031	0.00029	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.120

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.448

Gene Damage Prediction

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