POFUT2

protein O-fucosyltransferase 2, the group of Fucosyltransferases

Basic information

Region (hg38): 21:45263928-45287898

Previous symbols: [ "C21orf80" ]

Links

ENSG00000186866 ∙ NCBI:23275 ∙ OMIM:610249 ∙ HGNC:14683 ∙ Uniprot:Q9Y2G5 ∙ 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 POFUT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POFUT2 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				1		1
missense			27	1	2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	28	2	2

Variants in POFUT2

This is a list of pathogenic ClinVar variants found in the POFUT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-45265486-T-C		not specified	Uncertain significance (Oct 29, 2024)
21-45265520-C-T		not specified	Uncertain significance (Dec 05, 2022)
21-45265555-G-A		not specified	Uncertain significance (May 25, 2022)
21-45265635-C-T			Benign (Jun 26, 2018)
21-45267633-C-G		not specified	Uncertain significance (Apr 12, 2022)
21-45267662-G-A		not specified	Uncertain significance (Dec 07, 2024)
21-45267680-A-G		not specified	Uncertain significance (May 30, 2023)
21-45267684-C-T		not specified	Uncertain significance (Dec 21, 2022)
21-45269881-G-A			Benign (Jul 31, 2018)
21-45269901-C-T		not specified	Uncertain significance (Oct 25, 2023)
21-45269937-T-A		not specified	Uncertain significance (Dec 11, 2024)
21-45270002-C-T			Likely benign (Nov 01, 2022)
21-45270005-G-A		not specified	Likely benign (Feb 12, 2025)
21-45277109-G-A		not specified	Uncertain significance (Dec 05, 2024)
21-45277127-C-T		not specified	Uncertain significance (Mar 30, 2024)
21-45277136-G-A		not specified	Uncertain significance (Jul 26, 2022)
21-45277138-C-T		not specified	Uncertain significance (Aug 11, 2022)
21-45278119-C-T		not specified	Uncertain significance (Oct 26, 2022)
21-45282352-G-C		not specified	Uncertain significance (Sep 26, 2023)
21-45282383-C-T		not specified	Uncertain significance (May 17, 2023)
21-45282398-C-T		not specified	Uncertain significance (Jun 11, 2021)
21-45282419-C-T		not specified	Uncertain significance (Jul 21, 2021)
21-45282435-C-G		not specified	Uncertain significance (Jul 16, 2024)
21-45282445-C-T		not specified	Uncertain significance (Nov 19, 2024)
21-45283438-C-T		not specified	Uncertain significance (Jan 21, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POFUT2	protein_coding	protein_coding	ENST00000349485	9	23971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000216	0.996	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	204	256	0.796	0.0000160	2775
Missense in Polyphen		67	99.591	0.67275		1083
Synonymous	-1.65	134	112	1.20	0.00000816	827
Loss of Function	2.52	10	23.1	0.433	0.00000107	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.000106	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000622	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.000138	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the reaction that attaches fucose through an O-glycosidic linkage to a conserved serine or threonine residue in the consensus sequence C1-X(2,3)-S/T-C2-X(2)-G of thrombospondin type 1 repeats where C1 and C2 are the first and second cysteines, respectively. O-fucosylates members of several protein families including the ADAMTS family, the thrombosporin (TSP) and spondin families. The O-fucosylation of TSRs is also required for restricting epithelial to mesenchymal transition (EMT), maintaining the correct patterning of mesoderm and localization of the definite endoderm (By similarity). Required for the proper secretion of ADAMTS family members such as ADAMSL1 and ADAMST13. {ECO:0000250, ECO:0000269|PubMed:11067851, ECO:0000269|PubMed:16464858, ECO:0000269|PubMed:17395588, ECO:0000269|PubMed:17395589, ECO:0000269|PubMed:22588082}.
• Pathway: Other types of O-glycan biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.151

Intolerance Scores

• loftool: 0.275
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.49

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.488
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.696

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pofut2
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); embryo phenotype

Zebrafish Information Network

• Gene name: pofut2
• Affected structure: cranial nerve X
• Phenotype tag: abnormal
• Phenotype quality: position

Gene ontology

• Biological process: mesoderm formation;fucose metabolic process;regulation of gene expression;regulation of epithelial to mesenchymal transition;protein O-linked fucosylation;regulation of secretion
• Cellular component: endoplasmic reticulum membrane;Golgi apparatus
• Molecular function: peptide-O-fucosyltransferase activity