EXTL1

exostosin like glycosyltransferase 1, the group of Exostosin glycosyltransferase family

Basic information

Region (hg38): 1:26019884-26036464

Links

ENSG00000158008NCBI:2134OMIM:601738HGNC:3515Uniprot:Q92935AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EXTL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXTL1 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
40
clinvar
3
clinvar
43
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 40 3 0

Variants in EXTL1

This is a list of pathogenic ClinVar variants found in the EXTL1 region.

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

Position Type Phenotype Significance ClinVar
1-26022696-C-T not specified Uncertain significance (Apr 07, 2023)2565108
1-26022731-C-T not specified Uncertain significance (Jun 17, 2024)3276869
1-26022738-G-A not specified Uncertain significance (Nov 15, 2021)2325590
1-26022761-C-T not specified Uncertain significance (Dec 08, 2023)3091281
1-26022789-G-A not specified Uncertain significance (Mar 21, 2023)2522693
1-26022863-C-G not specified Uncertain significance (Aug 06, 2021)3091288
1-26022938-G-C not specified Uncertain significance (May 31, 2023)2553350
1-26022944-G-A not specified Uncertain significance (Dec 16, 2022)2336207
1-26022954-C-A not specified Uncertain significance (Mar 31, 2023)2531710
1-26022963-C-T not specified Uncertain significance (Dec 27, 2023)3091289
1-26022984-G-A not specified Likely benign (Oct 18, 2021)2255758
1-26022993-C-T not specified Uncertain significance (Jan 19, 2022)2272196
1-26023011-G-A not specified Uncertain significance (Aug 12, 2022)2210279
1-26023142-C-T not specified Uncertain significance (Feb 10, 2023)2462869
1-26023262-C-A not specified Uncertain significance (Apr 20, 2024)3276871
1-26023269-G-A not specified Uncertain significance (Oct 03, 2023)3091290
1-26023292-C-T not specified Uncertain significance (Nov 10, 2022)2390060
1-26023305-C-T not specified Uncertain significance (Aug 16, 2021)2215833
1-26023392-A-G not specified Uncertain significance (Feb 23, 2023)2488511
1-26029210-C-A not specified Uncertain significance (Mar 18, 2024)3276864
1-26029219-A-G not specified Uncertain significance (Dec 21, 2023)3091291
1-26029607-G-T not specified Uncertain significance (Apr 18, 2023)2538470
1-26029630-C-T not specified Uncertain significance (Dec 01, 2022)2364830
1-26029690-G-A not specified Uncertain significance (Oct 14, 2023)3091292
1-26029695-G-C not specified Uncertain significance (Feb 27, 2024)3091293

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EXTL1protein_codingprotein_codingENST00000374280 1116581
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
7.31e-120.41512539913471257470.00138
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9043363860.8710.00002154295
Missense in Polyphen114147.780.771431780
Synonymous0.1711601630.9830.000009181459
Loss of Function1.222127.90.7520.00000128303

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002950.00283
Ashkenazi Jewish0.002160.00169
East Asian0.0001090.000109
Finnish0.00004670.0000462
European (Non-Finnish)0.002150.00211
Middle Eastern0.0001090.000109
South Asian0.0006990.000653
Other0.001980.00196

dbNSFP

Source: dbNSFP

Function
FUNCTION: Probable glycosyltransferase. {ECO:0000250}.;
Pathway
Glycosaminoglycan biosynthesis - heparan sulfate / heparin - Homo sapiens (human);HH-Ncore;XBP1(S) activates chaperone genes;heparan sulfate biosynthesis (late stages);heparan sulfate biosynthesis (Consensus)

Recessive Scores

pRec
0.0936

Intolerance Scores

loftool
0.179
rvis_EVS
0.71
rvis_percentile_EVS
85.82

Haploinsufficiency Scores

pHI
0.199
hipred
N
hipred_score
0.170
ghis
0.517

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.666

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Extl1
Phenotype

Gene ontology

Biological process
skeletal system development;protein glycosylation;IRE1-mediated unfolded protein response
Cellular component
endoplasmic reticulum membrane;integral component of membrane
Molecular function
glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity