GCNT2

glucosaminyl (N-acetyl) transferase 2 (I blood group), the group of Glucosaminyl (N-acetyl) transferases/xylosyltransferases|Blood group antigens

Basic information

Region (hg38): 6:10492222-10629368

Previous symbols: [ "NACGT1", "II", "GCNT5", "CCAT" ]

Links

ENSG00000111846 ∙ NCBI:2651 ∙ OMIM:600429 ∙ HGNC:4204 ∙ Uniprot:Q8N0V5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract 13 with adult I phenotype (Moderate), mode of inheritance: AR
• total early-onset cataract (Supportive), mode of inheritance: AD
• cataract 13 with adult I phenotype (Definitive), mode of inheritance: AR
• cataract 13 with adult I phenotype (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, Ii; Adult i phenotype without cataract	BG/AR	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic; Ophthalmologic	6858080; 3799539; 11739194; 12424189; 21912254

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GCNT2 gene.

• Blood group, I system (89 variants)
• not provided (39 variants)
• Cataract 13 with adult I phenotype (27 variants)
• Inborn genetic diseases (12 variants)
• Adult i blood group with or without congenital cataract (6 variants)
• not specified (4 variants)
• GCNT2-related condition (1 variants)
• Cataract 13 with adult I phenotype;Blood group, I system (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCNT2 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	5	5	13
missense	1	1	31	2	4	39
nonsense	2		2			4
start loss						0
frameshift	2		3			5
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			48	16	30	94
Total	5	1	88	23	39

Highest pathogenic variant AF is 0.000315

Variants in GCNT2

This is a list of pathogenic ClinVar variants found in the GCNT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-10509132-C-T			Uncertain significance (Oct 01, 2022)
6-10528561-T-C			Benign (Jun 29, 2018)
6-10528781-A-G			Benign (Oct 01, 2018)
6-10528854-T-C			Benign (Oct 02, 2018)
6-10528886-A-C			Benign (Jun 29, 2018)
6-10528925-G-A		Cataract 13 with adult I phenotype	Pathogenic (May 06, 2021)
6-10529216-C-G		GCNT2-related disorder	Benign/Likely benign (Apr 09, 2019)
6-10529258-C-T		Inborn genetic diseases	Uncertain significance (Nov 09, 2021)
6-10529336-A-T		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)
6-10529416-G-A		ADULT i BLOOD GROUP PHENOTYPE	Pathogenic (Mar 15, 2003)
6-10529469-T-G		Cataract 13 with adult I phenotype	Uncertain significance (Feb 08, 2022)
6-10529478-C-G		Inborn genetic diseases	Uncertain significance (Aug 23, 2021)
6-10529528-A-G		Inborn genetic diseases	Uncertain significance (Oct 12, 2021)
6-10529551-A-C		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
6-10529594-G-A		ADULT i BLOOD GROUP PHENOTYPE	Pathogenic (Mar 15, 2003)
6-10529605-G-A		Inborn genetic diseases	Uncertain significance (Nov 05, 2021)
6-10529640-C-T		GCNT2-related disorder	Likely benign (Nov 04, 2021)
6-10529731-G-A		GCNT2-related disorder	Benign (Oct 28, 2019)
6-10529757-C-T		GCNT2-related disorder	Likely benign (Sep 01, 2022)
6-10529772-C-G		GCNT2-related disorder	Likely benign (May 22, 2019)
6-10529773-T-C		Inborn genetic diseases	Uncertain significance (Jul 14, 2021)
6-10529803-G-A		GCNT2-related disorder	Likely benign (Feb 10, 2022)
6-10529940-C-A			Likely benign (Jul 31, 2018)
6-10530003-A-T			Likely benign (Mar 24, 2019)
6-10555655-G-A			Benign (Jul 31, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCNT2	protein_coding	protein_coding	ENST00000379597	3	137146

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000241	0.761	125589	0	159	125748	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.10	262	216	1.21	0.0000120	2643
Missense in Polyphen		72	64.981	1.108		830
Synonymous	-1.28	105	89.6	1.17	0.00000578	783
Loss of Function	1.14	9	13.5	0.665	6.53e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00201	0.00201
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00261	0.00261
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.00261	0.00261
South Asian	0.00105	0.00105
Other	0.000977	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Branching enzyme that converts linear into branched poly-N-acetyllactosaminoglycans. Introduces the blood group I antigen during embryonic development. It is closely associated with the development and maturation of erythroid cells. {ECO:0000269|PubMed:7579796, ECO:0000269|PubMed:8449405}.
• Disease: DISEASE: Cataract 13, with adult i phenotype (CTRCT13) [MIM:116700]: An opacification of the crystalline lens of the eye that frequently results in visual impairment or blindness. Opacities vary in morphology, are often confined to a portion of the lens, and may be static or progressive. In general, the more posteriorly located and dense an opacity, the greater the impact on visual function. CTRCT13 is associated with the rare adult i phenotype, in which adult red blood cells are rich in i antigen and contain low levels of I antigen. {ECO:0000269|PubMed:11739194}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Glycosphingolipid biosynthesis - lacto and neolacto series - Homo sapiens (human);Glycosphingolipid biosynthesis - neolactoseries;terminal <i>O</i>-glycans residues modification (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.977
• rvis_EVS: -1.3
• rvis_percentile_EVS: 4.95

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.180
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.414

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gcnt2
• Phenotype: renal/urinary system phenotype; immune system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: glycosaminoglycan biosynthetic process;protein glycosylation;transforming growth factor beta receptor signaling pathway;multicellular organism development;positive regulation of cell population proliferation;posttranscriptional regulation of gene expression;positive regulation of epithelial to mesenchymal transition;negative regulation of cell-substrate adhesion;positive regulation of cell migration;positive regulation of heterotypic cell-cell adhesion;maintenance of lens transparency;positive regulation of protein kinase B signaling;positive regulation of ERK1 and ERK2 cascade
• Cellular component: Golgi membrane;cellular_component;Golgi apparatus;membrane;integral component of membrane
• Molecular function: N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity