rs1557042824

Variant names:

• chrX-48905133-GCCACGGCGGTACCCTCAGCCCACCAGAGCCCCACCAGGCCCAGTGCTGTGCCGAAGAGGCCCAGTTGCAGGTTGCGCAGCCACACGGAGCCTGAGCTGCCTTTGAGGATCTTCTCAAAGTAGACACCTGCGAAGCCGGAGGAGAGACAGGAGGCCACGACGGCTGCCAGGCCTGCCCCAGGGTTCTGATCCAGTGGCCGTGGGCCTCCCCCACCGGCTTGCTGTGCCTGGACAATGGCGACGCCAGTGAAGAGGAGCAGCAGGGAGGCCCACTGCAGCCGGGAAAGGCTGCGATTCAGCATGAGCACGGAGAACAGCGCTGTGGTCAGGATCTTCAGCTGGTATGTCACCTGCGAGTGGCACGTGGAAGGCACTGAGGGCTGACCCTGGCCCCCAACAGGTGCACATGGGGGGCAGCACCCACTGTGGGCCCCCAGGCACAATGGAGGGACAGGGTGGGGGGTATGACAGCAAAAACAGCAAAAGGAGCCAGCCACTGGCCATTGGCTGAGCTGCAGCAAAACAGTTCTGAAGTCTCTCCCAGCAAGTGCACAAAAGGATGGCTGTGCCAAGAAGTCCACATCCCAATCCCATTTCCTGGCTGTGTGACTGGGGACAAAGCACTTGCCCTGTCTGAGCCCTGGCATCATCATCTATAAAAGATGGCTGAGGTATGGAAGTATCTTTGTGATGAGGGACTTGATACAAATGAATCAATAGCCACAACAATGTCAGCAAATACTTACATAGTGCTTACAATATATCAGTGTGGTTCTAGGCACTGCACGTGAATTCATTCATTTAATTCTCACAACACCATTCTGAAGTGAGCACCACTGTAAGCCCCAATTTAAAGGTGAGAAAACTAAGGCACAGAGAGGTTAGGTGACGTGCCCCAAAATCACACAGCTGGAAGGTAGCAGAGCTGAGATTTGAACCCAGACAGCCTGGCCCCAGAATCCAGGCTCTTTAA-G
• rs1557042824
• NM_005660.3:c.426+287_775del

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_Strong PM2 PP5_Moderate

The NM_005660.3(SLC35A2):​c.426+287_775del​(p.Val143fs) variant causes a frameshift, splice acceptor, splice region, intron change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: SLC35A2 NM_005660.3 frameshift, splice_acceptor, splice_region, intron
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 6.16

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 5 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-48905133-GCCACGGCGGTACCCTCAGCCCACCAGAGCCCCACCAGGCCCAGTGCTGTGCCGAAGAGGCCCAGTTGCAGGTTGCGCAGCCACACGGAGCCTGAGCTGCCTTTGAGGATCTTCTCAAAGTAGACACCTGCGAAGCCGGAGGAGAGACAGGAGGCCACGACGGCTGCCAGGCCTGCCCCAGGGTTCTGATCCAGTGGCCGTGGGCCTCCCCCACCGGCTTGCTGTGCCTGGACAATGGCGACGCCAGTGAAGAGGAGCAGCAGGGAGGCCCACTGCAGCCGGGAAAGGCTGCGATTCAGCATGAGCACGGAGAACAGCGCTGTGGTCAGGATCTTCAGCTGGTATGTCACCTGCGAGTGGCACGTGGAAGGCACTGAGGGCTGACCCTGGCCCCCAACAGGTGCACATGGGGGGCAGCACCCACTGTGGGCCCCCAGGCACAATGGAGGGACAGGGTGGGGGGTATGACAGCAAAAACAGCAAAAGGAGCCAGCCACTGGCCATTGGCTGAGCTGCAGCAAAACAGTTCTGAAGTCTCTCCCAGCAAGTGCACAAAAGGATGGCTGTGCCAAGAAGTCCACATCCCAATCCCATTTCCTGGCTGTGTGACTGGGGACAAAGCACTTGCCCTGTCTGAGCCCTGGCATCATCATCTATAAAAGATGGCTGAGGTATGGAAGTATCTTTGTGATGAGGGACTTGATACAAATGAATCAATAGCCACAACAATGTCAGCAAATACTTACATAGTGCTTACAATATATCAGTGTGGTTCTAGGCACTGCACGTGAATTCATTCATTTAATTCTCACAACACCATTCTGAAGTGAGCACCACTGTAAGCCCCAATTTAAAGGTGAGAAAACTAAGGCACAGAGAGGTTAGGTGACGTGCCCCAAAATCACACAGCTGGAAGGTAGCAGAGCTGAGATTTGAACCCAGACAGCCTGGCCCCAGAATCCAGGCTCTTTAA-G is Pathogenic according to our data. Variant chrX-48905133-GCCACGGCGGTACCCTCAGCCCACCAGAGCCCCACCAGGCCCAGTGCTGTGCCGAAGAGGCCCAGTTGCAGGTTGCGCAGCCACACGGAGCCTGAGCTGCCTTTGAGGATCTTCTCAAAGTAGACACCTGCGAAGCCGGAGGAGAGACAGGAGGCCACGACGGCTGCCAGGCCTGCCCCAGGGTTCTGATCCAGTGGCCGTGGGCCTCCCCCACCGGCTTGCTGTGCCTGGACAATGGCGACGCCAGTGAAGAGGAGCAGCAGGGAGGCCCACTGCAGCCGGGAAAGGCTGCGATTCAGCATGAGCACGGAGAACAGCGCTGTGGTCAGGATCTTCAGCTGGTATGTCACCTGCGAGTGGCACGTGGAAGGCACTGAGGGCTGACCCTGGCCCCCAACAGGTGCACATGGGGGGCAGCACCCACTGTGGGCCCCCAGGCACAATGGAGGGACAGGGTGGGGGGTATGACAGCAAAAACAGCAAAAGGAGCCAGCCACTGGCCATTGGCTGAGCTGCAGCAAAACAGTTCTGAAGTCTCTCCCAGCAAGTGCACAAAAGGATGGCTGTGCCAAGAAGTCCACATCCCAATCCCATTTCCTGGCTGTGTGACTGGGGACAAAGCACTTGCCCTGTCTGAGCCCTGGCATCATCATCTATAAAAGATGGCTGAGGTATGGAAGTATCTTTGTGATGAGGGACTTGATACAAATGAATCAATAGCCACAACAATGTCAGCAAATACTTACATAGTGCTTACAATATATCAGTGTGGTTCTAGGCACTGCACGTGAATTCATTCATTTAATTCTCACAACACCATTCTGAAGTGAGCACCACTGTAAGCCCCAATTTAAAGGTGAGAAAACTAAGGCACAGAGAGGTTAGGTGACGTGCCCCAAAATCACACAGCTGGAAGGTAGCAGAGCTGAGATTTGAACCCAGACAGCCTGGCCCCAGAATCCAGGCTCTTTAA-G is described in ClinVar as [Pathogenic]. Clinvar id is 412239.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A2	NM_005660.3	c.426+287_775del	p.Val143fs	frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant	Exon 4 of 5	ENST00000247138.11	NP_005651.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35A2	ENST00000247138.11	c.426+287_775del	p.Val143fs	frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant	Exon 4 of 5	1	NM_005660.3	ENSP00000247138.5

Frequencies

GnomAD3 genomes Cov.: 23

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

SLC35A2-congenital disorder of glycosylation Pathogenic:1

Feb 17, 2017

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is a gross deletion of the genomic region encompassing a portion of intron 3 and exon 4 of the SLC35A2 gene (c.426+287_775del). While this deletion is not anticipated to result in nonsense mediated decay, it is expected to result in a truncated SLC35A2 protein lacking most or all of the residues encoded by exon 4 (~67% of the protein). While this particular variant has not been reported in the literature, several de novo missense and truncating variants in exon 4 have been reported in individuals affected with congenital disorders of glycosylation (PMID: 25262651, 24115232), suggesting that this region is important for protein function. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1557042824; hg19: chrX-48762410;