EXTL2

exostosin like glycosyltransferase 2, the group of Exostosin glycosyltransferase family

Basic information

Region (hg38): 1:100872372-100895179

Links

ENSG00000162694 ∙ NCBI:2135 ∙ OMIM:602411 ∙ HGNC:3516 ∙ Uniprot:Q9UBQ6 ∙ 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 EXTL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXTL2 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						0
missense			19	3		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	0

Variants in EXTL2

This is a list of pathogenic ClinVar variants found in the EXTL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-100874040-T-G		not specified	Uncertain significance (Sep 22, 2023)
1-100874101-A-T		not specified	Uncertain significance (May 11, 2022)
1-100874130-T-C		not specified	Uncertain significance (Aug 06, 2024)
1-100874149-T-C		not specified	Uncertain significance (Sep 24, 2024)
1-100874172-G-T		not specified	Uncertain significance (Nov 10, 2024)
1-100874231-G-A		not specified	Uncertain significance (Feb 07, 2025)
1-100874247-G-A		not specified	Uncertain significance (Nov 25, 2024)
1-100874275-G-T		not specified	Uncertain significance (Jan 21, 2025)
1-100874313-A-G		not specified	Uncertain significance (Aug 01, 2024)
1-100874370-T-C		not specified	Likely benign (Nov 21, 2024)
1-100876805-A-C		not specified	Uncertain significance (Dec 12, 2023)
1-100876825-G-A		not specified	Uncertain significance (Jan 04, 2024)
1-100877553-A-G		not specified	Uncertain significance (May 08, 2023)
1-100877589-G-T		not specified	Uncertain significance (Apr 26, 2023)
1-100877592-G-A		not specified	Uncertain significance (Oct 09, 2024)
1-100877641-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-100877644-C-T		not specified	Likely benign (Nov 09, 2023)
1-100877722-T-A		not specified	Likely benign (Jun 22, 2024)
1-100877754-C-T		not specified	Uncertain significance (Jan 17, 2025)
1-100877796-G-A		not specified	Uncertain significance (Dec 12, 2022)
1-100877820-A-G		not specified	Uncertain significance (Apr 23, 2024)
1-100877827-C-T		not specified	Uncertain significance (Jun 28, 2024)
1-100877856-A-G		not specified	Uncertain significance (Feb 01, 2025)
1-100877863-T-C		not specified	Uncertain significance (Feb 14, 2025)
1-100877877-C-T		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXTL2	protein_coding	protein_coding	ENST00000370114	4	23612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000176	0.898	125648	0	36	125684	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.831	146	177	0.824	0.00000835	2188
Missense in Polyphen		51	66.509	0.76682		871
Synonymous	0.315	58	61.1	0.949	0.00000289	621
Loss of Function	1.49	8	14.0	0.571	8.67e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000127
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000151	0.000150
Middle Eastern	0.000381	0.000381
South Asian	0.000262	0.000261
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycosyltransferase required for the biosynthesis of heparan-sulfate and responsible for the alternating addition of beta-1-4-linked glucuronic acid (GlcA) and alpha-1-4-linked N- acetylglucosamine (GlcNAc) units to nascent heparan sulfate chains. {ECO:0000269|PubMed:10318803}.
• Pathway: Glycosaminoglycan biosynthesis - heparan sulfate / heparin - Homo sapiens (human);XBP1(S) activates chaperone genes;Proteoglycan biosynthesis;heparan sulfate biosynthesis (late stages);heparan sulfate biosynthesis (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.387
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.553
• hipred: N
• hipred_score: 0.306
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.107

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Extl2
• Phenotype: cellular phenotype

Gene ontology

• Biological process: N-acetylglucosamine metabolic process;protein glycosylation;heparan sulfate proteoglycan biosynthetic process;UDP-N-acetylgalactosamine metabolic process;IRE1-mediated unfolded protein response
• Cellular component: extracellular region;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity;glycosaminoglycan binding;manganese ion binding;alpha-1,4-N-acetylgalactosaminyltransferase activity;glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity