EXTL1

exostosin like glycosyltransferase 1, the group of Exostosin glycosyltransferase family

Basic information

Region (hg38): 1:26019884-26036464

Links

ENSG00000158008 ∙ NCBI:2134 ∙ OMIM:601738 ∙ HGNC:3515 ∙ Uniprot:Q92935 ∙ 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 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	3		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)
1-26022731-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-26022738-G-A		not specified	Uncertain significance (Nov 15, 2021)
1-26022761-C-T		not specified	Uncertain significance (Dec 08, 2023)
1-26022789-G-A		not specified	Uncertain significance (Mar 21, 2023)
1-26022863-C-G		not specified	Uncertain significance (Aug 06, 2021)
1-26022938-G-C		not specified	Uncertain significance (May 31, 2023)
1-26022944-G-A		not specified	Uncertain significance (Dec 16, 2022)
1-26022954-C-A		not specified	Uncertain significance (Mar 31, 2023)
1-26022963-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-26022984-G-A		not specified	Likely benign (Oct 18, 2021)
1-26022993-C-T		not specified	Uncertain significance (Jan 19, 2022)
1-26023011-G-A		not specified	Uncertain significance (Aug 12, 2022)
1-26023142-C-T		not specified	Uncertain significance (Feb 10, 2023)
1-26023262-C-A		not specified	Uncertain significance (Apr 20, 2024)
1-26023269-G-A		not specified	Uncertain significance (Oct 03, 2023)
1-26023292-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-26023305-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-26023392-A-G		not specified	Uncertain significance (Feb 23, 2023)
1-26029210-C-A		not specified	Uncertain significance (Mar 18, 2024)
1-26029219-A-G		not specified	Uncertain significance (Dec 21, 2023)
1-26029607-G-T		not specified	Uncertain significance (Apr 18, 2023)
1-26029630-C-T		not specified	Uncertain significance (Dec 01, 2022)
1-26029690-G-A		not specified	Uncertain significance (Oct 14, 2023)
1-26029695-G-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXTL1	protein_coding	protein_coding	ENST00000374280	11	16581

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.31e-12	0.415	125399	1	347	125747	0.00138

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.904	336	386	0.871	0.0000215	4295
Missense in Polyphen		114	147.78	0.77143		1780
Synonymous	0.171	160	163	0.983	0.00000918	1459
Loss of Function	1.22	21	27.9	0.752	0.00000128	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00295	0.00283
Ashkenazi Jewish	0.00216	0.00169
East Asian	0.000109	0.000109
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.00215	0.00211
Middle Eastern	0.000109	0.000109
South Asian	0.000699	0.000653
Other	0.00198	0.00196

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

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

Mouse Genome Informatics

• Gene name: Extl1

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