2-106098758-G-A

Variant names:

• chr2-106098758-G-A
• rs899726824
• NM_001253875.2:c.1000C>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001253875.2(UXS1):​c.1000C>T​(p.His334Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,378 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: UXS1 NM_001253875.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.74

Genes affected

UXS1 (HGNC:17729): (UDP-glucuronate decarboxylase 1) This gene encodes an enzyme found in the perinuclear Golgi which catalyzes the synthesis of UDP-xylose used in glycosaminoglycan (GAG) synthesis on proteoglycans. The GAG chains are covalently attached to proteoglycans which participate in signaling pathways during development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UXS1	NM_001253875.2	c.1000C>T	p.His334Tyr	missense_variant	Exon 13 of 15	ENST00000283148.12	NP_001240804.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UXS1	ENST00000283148.12	c.1000C>T	p.His334Tyr	missense_variant	Exon 13 of 15	2	NM_001253875.2	ENSP00000283148.7
UXS1	ENST00000409501.7	c.985C>T	p.His329Tyr	missense_variant	Exon 13 of 15	1		ENSP00000387019.3
UXS1	ENST00000409032.5	c.481C>T	p.His161Tyr	missense_variant	Exon 8 of 10	1		ENSP00000387096.1
UXS1	ENST00000497604.1	n.1911C>T		non_coding_transcript_exon_variant	Exon 2 of 4	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1459378 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 725742

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Oct 04, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.985C>T (p.H329Y) alteration is located in exon 13 (coding exon 13) of the UXS1 gene. This alteration results from a C to T substitution at nucleotide position 985, causing the histidine (H) at amino acid position 329 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Pathogenic	0.32	D
BayesDel_noAF	Pathogenic	0.22
CADD	Benign	23
DANN	Benign	0.95
DEOGEN2	Uncertain	0.62	.;D;.
Eigen	Benign	-0.34
Eigen_PC	Benign	-0.088
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.98	D;D;D
M_CAP	Benign	0.073	D
MetaRNN	Uncertain	0.49	T;T;T
MetaSVM	Uncertain	-0.038	T
MutationAssessor	Benign	-0.33	.;N;.
PrimateAI	Pathogenic	0.87	D
PROVEAN	Benign	-1.9	N;N;N
REVEL	Uncertain	0.54
Sift	Benign	0.44	T;T;T
Sift4G	Benign	0.34	T;T;T
Polyphen		0.016	B;B;.
Vest4		0.71
MutPred		0.37		.;Loss of disorder (P = 0.0441);.;
MVP		0.74
MPC		0.85
ClinPred		0.87	D
GERP RS		4.6
Varity_R		0.41
gMVP		0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs899726824; hg19: chr2-106715214;