3-195070052-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152531.5(XXYLT1):āc.845C>Gā(p.Pro282Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,597,990 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00016 ( 0 hom., cov: 33)
Exomes š: 0.00012 ( 0 hom. )
Consequence
XXYLT1
NM_152531.5 missense
NM_152531.5 missense
Scores
4
7
8
Clinical Significance
Conservation
PhyloP100: 8.07
Genes affected
XXYLT1 (HGNC:26639): (xyloside xylosyltransferase 1) Enables magnesium ion binding activity; manganese ion binding activity; and xylosyl alpha-1,3-xylosyltransferase activity. Involved in O-glycan processing. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XXYLT1 | NM_152531.5 | c.845C>G | p.Pro282Arg | missense_variant | 4/4 | ENST00000310380.11 | NP_689744.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XXYLT1 | ENST00000310380.11 | c.845C>G | p.Pro282Arg | missense_variant | 4/4 | 1 | NM_152531.5 | ENSP00000309640.6 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152244Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000187 AC: 43AN: 229828Hom.: 0 AF XY: 0.000213 AC XY: 27AN XY: 126718
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GnomAD4 exome AF: 0.000125 AC: 180AN: 1445746Hom.: 0 Cov.: 32 AF XY: 0.000129 AC XY: 93AN XY: 719584
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GnomAD4 genome AF: 0.000158 AC: 24AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74376
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2022 | The c.845C>G (p.P282R) alteration is located in exon 4 (coding exon 4) of the XXYLT1 gene. This alteration results from a C to G substitution at nucleotide position 845, causing the proline (P) at amino acid position 282 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
T;.;T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D
REVEL
Uncertain
Sift
Benign
T;T;T;T
Sift4G
Benign
T;T;T;T
Polyphen
D;D;.;D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at