rs397514546
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Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_014254.3(RXYLT1):c.279delA(p.Gly94fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,088 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
RXYLT1
NM_014254.3 frameshift
NM_014254.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.959
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 Pathogenic. Variant got 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 12-63781125-GA-G is Pathogenic according to our data. Variant chr12-63781125-GA-G is described in ClinVar as [Pathogenic]. Clinvar id is 39607.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr12-63781125-GA-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RXYLT1 | NM_014254.3 | c.279delA | p.Gly94fs | frameshift_variant | 2/6 | ENST00000261234.11 | NP_055069.1 | |
RXYLT1 | XM_047428079.1 | c.279delA | p.Gly94fs | frameshift_variant | 2/5 | XP_047284035.1 | ||
RXYLT1 | NM_001278237.2 | c.-502delA | 5_prime_UTR_variant | 2/6 | NP_001265166.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RXYLT1 | ENST00000261234.11 | c.279delA | p.Gly94fs | frameshift_variant | 2/6 | 1 | NM_014254.3 | ENSP00000261234.6 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245692Hom.: 0 AF XY: 0.00000752 AC XY: 1AN XY: 133014
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GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455088Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 723804
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GnomAD4 genome Cov.: 33
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33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 07, 2012 | - - |
Computational scores
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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