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Fetal anomalies

STR: XYLT1_GCC

Red List (low evidence)
Chromosome: 16
GRCh38 Position: 17470907-17470922
Repeated Sequence: GCC
Normal Number of Repeats: < 20
Pathogenic Number of Repeats: = or > 110

XYLT1 (xylosyltransferase 1)
EnsemblGeneIds (GRCh38): ENSG00000103489
EnsemblGeneIds (GRCh37): ENSG00000103489
OMIM: 608124, Gene2Phenotype
XYLT1 is in 0 panels

2 reviews

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

R21 Clinical Oversight Group comment: Agree that this should be approved by the STR group first
Created: 12 Dec 2025, 12:34 p.m. | Last Modified: 12 Dec 2025, 12:34 p.m.
Panel Version: 6.117
Comment on list classification: There is sufficient evidence to support an association with Desbuquois dysplasia, however, this STR is currently not green on any panels as it has not been approved by the NHS STR working group and is not NGS validated. Therefore the Red rating will be maintained for now.
Created: 5 Sep 2025, 3:45 p.m. | Last Modified: 5 Sep 2025, 3:45 p.m.
Panel Version: 6.26
This STR and phenotype were reviewed during meetings in June & July 2025. The meetings included representatives of the North Thames and Central & South R21 testing GLHs and from the R21 Clinical Oversight Group. Clinical review and curation was performed by Natalie Chandler & Elizabeth Scotchman (North Thames GLH), Natalie Bibb, Stephanie Allen & Sarah Graham (Central & South GLH) and Alice Gardham, Esther Kinning, Vicki Harrison, Anna DeBurca, Natalie Canham, Elizabeth Wall, Sunayna Best, Soo-Mi Park & Sahar Mansour (R21 Clinical Oversight Group).
Created: 5 Sep 2025, 3:11 p.m. | Last Modified: 5 Sep 2025, 3:11 p.m.
Panel Version: 6.24
Green expert review added on behalf of Anna de Burca (Oxford University Hospitals NHS Foundation Trust), as part of a review of this panel by the R21 Clinical Oversight Group:

"XYLT1 is Green. SLB. Definitely appropriate for inclusion following transition to WGS, in the meantime monoallelic variants in XYLT1 be reported so STR testing can be performed."
Created: 5 Sep 2025, 3:08 p.m. | Last Modified: 5 Sep 2025, 3:08 p.m.
Panel Version: 6.24

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Desbuquois dysplasia 2, OMIM:615777

Publications

Created: 5 Sep 2025, 3:08 p.m.
Last Modified: 5 Sep 2025, 3:08 p.m.
Panel version: 6.117

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

XYLT1 transcribed from the reverse strand, which means that the repeated sequence is the reverse compliment of the forward strand sequence.

XYLT1_GCC is on https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r3

XYLT1_GCC is on https://stripy.org/database

XYLT1_GCC is on DRAGON 4.02.

The coordinates and pathogenic ranges of the sequence repeats were obtained from
https://gnomad.broadinstitute.org/short-tandem-repeats?dataset=gnomad_r3 and were the same on https://stripy.org/database/ and DRAGON 4.02/

There is enough evidence for XYLT1_GGC to be green on this panel. At least ten patients from at least eight families have either homozygous or compound heterozygous (with other XYLT1 variants) XYLT1_GGC expansions (PMID: 22711505;30554721).

This STR has not been approved by NHS STR working group and is not NGS Not Validated
Sources: Literature
Created: 19 Mar 2025, 2:41 p.m. | Last Modified: 19 Mar 2025, 2:42 p.m.
Panel Version: 7.30

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Desbuquois dysplasia 2, OMIM:615777; Desbuquois dysplasia 2, MONDO:0014343

Publications

Created: 19 Mar 2025, 2:41 p.m.
Last Modified: 19 Mar 2025, 2:42 p.m.
Copied from panel: Skeletal dysplasia v8.7

Details

Name
XYLT1_GCC
Chromosome
16
GRCh38 Coordinates
17470907-17470922
Repeated Sequence
GCC
Normal Number of Repeats: <
20
Pathogenic Number of Repeats: = or >
110
Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
  • Literature
Phenotypes
  • Desbuquois dysplasia 2, OMIM:615777
  • Desbuquois dysplasia 2, MONDO:0014343
Tags
STR NGS Not Validated
OMIM
608124
Clinvar variants
Variants in XYLT1
Penetrance
None
Publications

History Filter Activity

5 Sep 2025, Gel status: 1

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Str: xylt1_gcc has been classified as Red List (Low Evidence).

5 Sep 2025, Gel status: 1

Created, Added New Source, Added Tag, Set mode of inheritance, Set publications, Set Phenotypes

Arina Puzriakova (Genomics England Curator)

STR: XYLT1_GCC was added STR: XYLT1_GCC was added to Fetal anomalies. Sources: Literature STR, NGS Not Validated tags were added to STR: XYLT1_GCC. Mode of inheritance for STR: XYLT1_GCC was set to BIALLELIC, autosomal or pseudoautosomal Publications for STR: XYLT1_GCC were set to 22711505; 30554721 Phenotypes for STR: XYLT1_GCC were set to Desbuquois dysplasia 2, OMIM:615777; Desbuquois dysplasia 2, MONDO:0014343