rs1557044030
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_005660.3(SLC35A2):c.15_91+48delinsA variant causes a splice donor, splice donor 5th base, coding sequence, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 24)
Consequence
SLC35A2
NM_005660.3 splice_donor, splice_donor_5th_base, coding_sequence, intron
NM_005660.3 splice_donor, splice_donor_5th_base, coding_sequence, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.689
Genes affected
SLC35A2 (HGNC:11022): (solute carrier family 35 member A2) This gene encodes a member of the nucleotide-sugar transporter family. The encoded protein is a multi-pass membrane protein. It transports UDP-galactose from the cytosol into Golgi vesicles, where it serves as a glycosyl donor for the generation of glycans. Mutations in this gene cause congenital disorder of glycosylation type IIm (CDG2M). Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Oct 2014]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Splicing variant, LoF is a know mechanism of disease,
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant X-48911498-GATCCCGACCTCCGCCTCCCATGCGACTGCTCGGGCAGACTGTCTCACCCGCACTGGCGGTCCCCGGCTCCAATGCACCCGCGGAAACCGCCCCTGGCCCGGGCGCCGCGGTGGAACCACCAGCC-T is Pathogenic according to our data. Variant chrX-48911498-GATCCCGACCTCCGCCTCCCATGCGACTGCTCGGGCAGACTGTCTCACCCGCACTGGCGGTCCCCGGCTCCAATGCACCCGCGGAAACCGCCCCTGGCCCGGGCGCCGCGGTGGAACCACCAGCC-T is described in ClinVar as [Pathogenic]. Clinvar id is 50363.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35A2 | NM_005660.3 | c.15_91+48delinsA | splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 1/5 | ENST00000247138.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35A2 | ENST00000247138.11 | c.15_91+48delinsA | splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 1/5 | 1 | NM_005660.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 genomes
?
Cov.:
24
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 24
GnomAD4 genome
?
Cov.:
24
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SLC35A2-congenital disorder of glycosylation Pathogenic:2
Pathogenic, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | Nov 14, 2013 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 04, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at