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.

not_specified (28 variants)

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. These statistics are base on transcript: NM_001033025.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			25 clinvar	3 clinvar		28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	3	0

Loading clinvar variants...

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