rs536862073
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_014254.3(RXYLT1):c.1272G>A(p.Glu424=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,582,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
RXYLT1
NM_014254.3 synonymous
NM_014254.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.28
Genes affected
RXYLT1 (HGNC:13530): (ribitol xylosyltransferase 1) This gene encodes a type II transmembrane protein that is thought to have glycosyltransferase function. Mutations in this gene result in cobblestone lissencephaly. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.43).
BP6
?
Variant 12-63809032-G-A is Benign according to our data. Variant chr12-63809032-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 473412.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.28 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RXYLT1 | NM_014254.3 | c.1272G>A | p.Glu424= | synonymous_variant | 6/6 | ENST00000261234.11 | |
RXYLT1-AS1 | NR_126167.1 | n.468-92C>T | intron_variant, non_coding_transcript_variant | ||||
RXYLT1 | NM_001278237.2 | c.492G>A | p.Glu164= | synonymous_variant | 6/6 | ||
RXYLT1 | XM_047428078.1 | c.963G>A | p.Glu321= | synonymous_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RXYLT1 | ENST00000261234.11 | c.1272G>A | p.Glu424= | synonymous_variant | 6/6 | 1 | NM_014254.3 | P1 | |
RXYLT1-AS1 | ENST00000546214.1 | n.468-92C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152168Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000762 AC: 17AN: 223174Hom.: 0 AF XY: 0.0000902 AC XY: 11AN XY: 121928
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GnomAD4 exome AF: 0.000106 AC: 151AN: 1430812Hom.: 0 Cov.: 29 AF XY: 0.000107 AC XY: 76AN XY: 711754
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GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74340
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2022 | RXYLT1: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 18, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
RXYLT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 07, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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