rs761338090

Variant names:

• chr3-72955198-C-A
• rs761338090
• NM_001080393.2:c.701C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-72955198-C-A
• chr3-72955198-C-G

Variant summary

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

The NM_001080393.2(GXYLT2):​c.701C>A​(p.Ser234Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S234C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: GXYLT2 NM_001080393.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

Genes affected

GXYLT2 (HGNC:33383): (glucoside xylosyltransferase 2) The protein encoded by this gene is a xylosyltransferase that elongates O-linked glucose bound to epidermal growth factor (EGF) repeats. The encoded protein catalyzes the addition of xylose to the O-glucose-modified residues of EGF repeats of Notch proteins. [provided by RefSeq, Sep 2016]

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
GXYLT2	NM_001080393.2	c.701C>A	p.Ser234Tyr	missense_variant	Exon 4 of 7	ENST00000389617.9	NP_001073862.1
GXYLT2	NR_138564.2	n.889C>A		non_coding_transcript_exon_variant	Exon 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GXYLT2	ENST00000389617.9	c.701C>A	p.Ser234Tyr	missense_variant	Exon 4 of 7	5	NM_001080393.2	ENSP00000374268.4
GXYLT2	ENST00000491839.1	c.-17C>A		upstream_gene_variant		3		ENSP00000420426.1
GXYLT2	ENST00000498315.1	c.*17C>A		downstream_gene_variant		2		ENSP00000417239.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Benign	0.011	T
BayesDel_noAF	Benign	-0.22
CADD	Uncertain	26
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.63	D
Eigen	Uncertain	0.61
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Benign	0.54	D
LIST_S2	Uncertain	0.92	D
M_CAP	Benign	0.0067	T
MetaRNN	Uncertain	0.64	D
MetaSVM	Uncertain	0.062	D
MutationAssessor	Uncertain	2.2	M
PrimateAI	Uncertain	0.60	T
PROVEAN	Pathogenic	-5.0	D
REVEL	Benign	0.23
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0040	D
Polyphen		1.0	D
Vest4		0.58
MutPred		0.47		Loss of disorder (P = 0.0861);
MVP		0.74
MPC		0.70
ClinPred		0.98	D
GERP RS		5.3
Varity_R		0.50
gMVP		0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs761338090; hg19: chr3-73004349;